Science.gov

Sample records for gen agxt r197q

  1. [Primary hiperoxaluria: a new mutation in gen AGXT (R197Q) cause of neonatal convulsions].

    PubMed

    Guevara-Campos, José; Riverol, Débora; González-Guevara, Lucía; Tinedo, Rubin

    2008-12-01

    Primary hyperoxaluria is a congenital innate error of the metabolism of the amino acids, that is transmitted like an autosomal recessive character. Two types of hyperoxaluria exist: the primary type I, that corresponds to the peroxisomal enzymatic deficit of the alanine glyoxylate aminotransferase in the liver (AGT) and type II, due to the deficit of the glyoxylate reductase/hydroxypyruvate reductase deficiency (GRHPR). The primary type I (AGT) is the most frequenty. We report the case of a female infant of one month of age, that on her first day post birth, presented myoclonic convulsions and tonic spasms, both during wakefullness and sleep periods, that became more frequent and did not respond to the use of anticonvulsants. The ictal Electroencephalogram presented an intermittent activity of spikes and spike-waves of high voltage in the right hemisphere. Eight minutes after the intravenous administration of 150 mg of pyridoxine, it was observed a diminution of the epileptic activity, as well as the clinical manifestations. The determination of organic acids in urine revealed an increase in the concentration levels of oxalic acid (3064 mmol/mol of creatinine). The molecular genetic study of the AGXT gene, showed the existence of a R197Q mutation in exón 5 of the patient and her father. She received treatment with pyridoxine at a dose of 50 mg/day. When she reached the age of three months both a normal electroencephalogram and biochemistry were obtained. Although it is a rare cause of neonatal convulsions, hyperoxaluria, due to new mutations is an underdiagnosed disease by neonatologists and paediatricias. PMID:19245173

  2. GenBank.

    PubMed

    Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

    2016-01-01

    GenBank(®) (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 340 000 formally described species. Recent developments include a new starting page for submitters, a shift toward using accession.version identifiers rather than GI numbers, a wizard for submitting 16S rRNA sequences, and an Identical Protein Report to address growing issues of data redundancy. GenBank organizes the sequence data received from individual laboratories and large-scale sequencing projects into 18 divisions, and GenBank staff assign unique accession.version identifiers upon data receipt. Most submitters use the web-based BankIt or standalone Sequin programs. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the nuccore, nucest, and nucgss databases of the Entrez retrieval system, which integrates these records with a variety of other data including taxonomy nodes, genomes, protein structures, and biomedical journal literature in PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. PMID:26590407

  3. GenBank

    PubMed Central

    Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Sayers, Eric W.

    2016-01-01

    GenBank® (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 340 000 formally described species. Recent developments include a new starting page for submitters, a shift toward using accession.version identifiers rather than GI numbers, a wizard for submitting 16S rRNA sequences, and an Identical Protein Report to address growing issues of data redundancy. GenBank organizes the sequence data received from individual laboratories and large-scale sequencing projects into 18 divisions, and GenBank staff assign unique accession.version identifiers upon data receipt. Most submitters use the web-based BankIt or standalone Sequin programs. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the nuccore, nucest, and nucgss databases of the Entrez retrieval system, which integrates these records with a variety of other data including taxonomy nodes, genomes, protein structures, and biomedical journal literature in PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. PMID:26590407

  4. Using GenBank.

    PubMed

    Sayers, Eric W; Karsch-Mizrachi, Ilene

    2016-01-01

    GenBank(®) is a comprehensive database of publicly available DNA sequences for 300,000 named organisms, more than 110,000 within the embryophyta, obtained through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Daily data exchange with the European Nucleotide Archive (ENA) in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data from the major DNA and protein sequence databases with taxonomy, genome, mapping, protein structure and domain information, as well as the biomedical journal literature in PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. GenBank usage scenarios ranging from local analyses of the data available via FTP to online analyses supported by the NCBI web-based tools are discussed. To access GenBank and its related retrieval and analysis services, go to the NCBI home page at www.ncbi.nlm.nih.gov . PMID:26519398

  5. GenBank

    PubMed Central

    Burks, Christian; Cassidy, Maxxwell; Cinkosky, Michael J.; Cumella, Karen E.; Gilna, Paul; Hayden, Jamie E.-D.; Keen, Gifford M.; Kelley, Tom A.; Kelly, Michael; Kristofferson, David; Ryals, Julie

    1991-01-01

    The GenBank nucleotide sequence database now contains sequence data and associated annotation corresponding to 56,000,000 nucleotides in 45,000 entries. The input stream of data coming into the database has largely been shifted to direct submissions from the scientific community on electronic media. The data have been installed in a relational database management system and are made available in this form through on-line access, and through various network and off-line computer-readable media. In addition, GenBank provides the U.S. distribution center for the BIOSCI electronic bulletin board service. PMID:2041806

  6. Verifying Test Hypotheses -HOL/TestGen Verifying Test Hypotheses -HOL/TestGen

    E-print Network

    Verifying Test Hypotheses - HOL/TestGen Verifying Test Hypotheses - HOL/TestGen An Experiment in Test and Proof Thomas Malcher January 20, 2014 1 / 20 #12;Verifying Test Hypotheses - HOL/TestGen HOL/TestGen Outline Introduction Test Hypotheses HOL/TestGen - Demo Verifying Test Hypotheses Conclusion 2 / 20 #12

  7. Summary of CPAS Gen II Parachute Analysis

    NASA Technical Reports Server (NTRS)

    Morris, Aaron L.; Bledsoe, Kristin J.; Fraire, Usbaldo, Jr.; Moore, James W.; Olson, Leah M.; Ray, Eric

    2011-01-01

    The Orion spacecraft is currently under development by NASA and Lockheed Martin. Like Apollo, Orion will use a series of parachutes to slow its descent and splashdown safely. The Orion parachute system, known as the CEV Parachute Assembly System (CPAS), is being designed by NASA, the Engineering and Science Contract Group (ESCG), and Airborne Systems. The first generation (Gen I) of CPAS testing consisted of thirteen tests and was executed in the 2007-2008 timeframe. The Gen I tests provided an initial understanding of the CPAS parachutes. Knowledge gained from Gen I testing was used to plan the second generation of testing (Gen II). Gen II consisted of six tests: three singleparachute tests, designated as Main Development Tests, and three Cluster Development Tests. Gen II required a more thorough investigation into parachute performance than Gen I. Higher fidelity instrumentation, enhanced analysis methods and tools, and advanced test techniques were developed. The results of the Gen II test series are being incorporated into the CPAS design. Further testing and refinement of the design and model of parachute performance will occur during the upcoming third generation of testing (Gen III). This paper will provide an overview of the developments in CPAS analysis following the end of Gen I, including descriptions of new tools and techniques as well as overviews of the Gen II tests.

  8. FutureGen Project Report

    SciTech Connect

    Cabe, Jim; Elliott, Mike

    2010-09-30

    This report summarizes the comprehensive siting, permitting, engineering, design, and costing activities completed by the FutureGen Industrial Alliance, the Department of Energy, and associated supporting subcontractors to develop a first of a kind near zero emissions integrated gasification combined cycle power plant and carbon capture and storage project (IGCC-CCS). With the goal to design, build, and reliably operate the first IGCC-CCS facility, FutureGen would have been the lowest emitting pulverized coal power plant in the world, while providing a timely and relevant basis for coal combustion power plants deploying carbon capture in the future. The content of this report summarizes key findings and results of applicable project evaluations; modeling, design, and engineering assessments; cost estimate reports; and schedule and risk mitigation from initiation of the FutureGen project through final flow sheet analyses including capital and operating reports completed under DOE award DE-FE0000587. This project report necessarily builds upon previously completed siting, design, and development work executed under DOE award DE-FC26- 06NT4207 which included the siting process; environmental permitting, compliance, and mitigation under the National Environmental Policy Act; and development of conceptual and design basis documentation for the FutureGen plant. For completeness, the report includes as attachments the siting and design basis documents, as well as the source documentation for the following: • Site evaluation and selection process and environmental characterization • Underground Injection Control (UIC) Permit Application including well design and subsurface modeling • FutureGen IGCC-CCS Design Basis Document • Process evaluations and technology selection via Illinois Clean Coal Review Board Technical Report • Process flow diagrams and heat/material balance for slurry-fed gasifier configuration • Process flow diagrams and heat/material balance for dry-fed gasifier configuration • Full capital cost report and cost category analysis (CAPEX) • Full operating cost report and assumptions (OPEX) Comparative technology evaluations, value engineering exercises, and initial air permitting activities are also provided; the report concludes with schedule, risk, and cost mitigation activities as well as lessons learned such that the products of this report can be used to support future investments in utility scale gasification and carbon capture and sequestration. Collectively, the FutureGen project enabled the comprehensive site specific evaluation and determination of the economic viability of IGCC-CCS. The project report is bound at that determination when DOE formally proposed the FutureGen 2.0 project which focuses on repowering a pulverized coal power plant with oxy-combustion technology including CCS.

  9. Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend.

    PubMed

    Stackebrandt, E; Koch, C; Gvozdiak, O; Schumann, P

    1995-10-01

    The results of a phylogenetic and chemotaxonomic analysis of the genus Micrococcus indicated that it is significantly heterogeneous. Except for Micrococcus lylae, no species groups phylogenetically with the type species of the genus, Micrococcus luteus. The other members of the genus form three separate phylogenetic lines which on the basis of chemotaxonomic properties can be assigned to four genera. These genera are the genus Kocuria gen. nov. for Micrococcus roseus, Micrococcus varians, and Micrococcus kristinae, described as Kocuria rosea comb. nov., Kocuria varians comb. nov., and Kocuria kristinae comb. nov., respectively; the genus Nesterenkonia gen. nov. for Micrococcus halobius, described as Nesterenkonia halobia comb. nov.; the genus Nesterenkonia gen. nov. for Micrococcus halobius, described as Nesterenkonia halobia comb. nov.; the genus Dermacoccus gen. nov. for Micrococcus nishinomiyaensis, described as Dermacoccus nishinomiyaensis comb. nov.; and the genus Kytocossus gen. nov. for Micrococcus sedentarius, described as Kytococcus sedentarius comb. nov. M. luteus and M. lylae, which are closely related phylogenetically but differ in some chemotaxonomic properties, are the only species that remain in the genus Micrococcus Cohn 1872. An emended description of the genus Micrococcus is given [corrected]. PMID:7547287

  10. Gen. Ed. Req.MATH 1210 Calculus II

    E-print Network

    Provancher, William

    Gen. Ed. Req.MATH 1210 Calculus I MATH 1220 Calculus II MATH 2250 ODEs & Linear Algebra MATH 2210 Calculus III Gen. Ed. Req. MATH 3150 PDEs Gen. Ed. Req.Gen. Ed. Req. ME EN 1000 Intro to Design for Eng Sys in prereqs for MATH One repeat per course (second grade counts) Graduation Requirements U of U BS

  11. AutoGen Version 5.0

    NASA Technical Reports Server (NTRS)

    Gladden, Roy E.; Khanampornpan, Teerapat; Fisher, Forest W.

    2010-01-01

    Version 5.0 of the AutoGen software has been released. Previous versions, variously denoted Autogen and autogen, were reported in two articles: Automated Sequence Generation Process and Software (NPO-30746), Software Tech Briefs (Special Supplement to NASA Tech Briefs), September 2007, page 30, and Autogen Version 2.0 (NPO- 41501), NASA Tech Briefs, Vol. 31, No. 10 (October 2007), page 58. To recapitulate: AutoGen (now signifying automatic sequence generation ) automates the generation of sequences of commands in a standard format for uplink to spacecraft. AutoGen requires fewer workers than are needed for older manual sequence-generation processes, and greatly reduces sequence-generation times. The sequences are embodied in spacecraft activity sequence files (SASFs). AutoGen automates generation of SASFs by use of another previously reported program called APGEN. AutoGen encodes knowledge of different mission phases and of how the resultant commands must differ among the phases. AutoGen also provides means for customizing sequences through use of configuration files. The approach followed in developing AutoGen has involved encoding the behaviors of a system into a model and encoding algorithms for context-sensitive customizations of the modeled behaviors. This version of AutoGen addressed the MRO (Mars Reconnaissance Orbiter) primary science phase (PSP) mission phase. On previous Mars missions this phase has more commonly been referred to as mapping phase. This version addressed the unique aspects of sequencing orbital operations and specifically the mission specific adaptation of orbital operations for MRO. This version also includes capabilities for MRO s role in Mars relay support for UHF relay communications with the MER rovers and the Phoenix lander.

  12. Unleashing Gen Y: Marketing Mars to Millennials

    NASA Technical Reports Server (NTRS)

    Leahy, Bart D.; Hidalgo, Loretta; Kloberdanz, Cassie

    2007-01-01

    Space advocates need to engage Generation Y (born 1977-1999).This outreach is necessary to recruit the next generation of scientists and engineers to explore Mars. Space advocates in the non-profit, private, and government sectors need to use a combination of technical communication, marketing, and politics, to develop messages that resonate with Gen Y. Until now, space messages have been generated by and for college-educated white males; Gen Y is much more diverse, including as much as one third minorities. Young women, too, need to be reached. My research has shown that messages emphasizing technology, fun, humor, and opportunity are the best means of reaching the Gen Y audience of 60 million (US population is 300 million). The important things space advocates must avoid are talking down to this generation, making false promises, or expecting them to "wait their turn" before they can participate. This is the MTV generation! We need to find ways of engaging Gen Y now to build a future where human beings can live and work on the planet Mars. In addition to the messages themselves, advocates need to keep up with Gen Y' s social networking and use of iPods, cell phones, and the Internet. NASA and space advocacy groups can use these tools for "viral marketing," where young people share targeted space-related information via cell phones or the Internet because they like it. Overall, Gen Y is a socially dynamic and media-savvy group; advocates' space messages need to be sincere, creative, and placed in locations where Gen Y lives. Mars messages must be memorable!

  13. 24/04/2013 Next gen Sequencing technologies

    E-print Network

    Twente, Universiteit

    ;1985 Human genome project proposed Start of the project in 1987 24/04/2013Next gen Sequencing technologies 7 "next gen" patents filed 2003 Human genome project finished 2005 first next gen sequencer available The illumina sequencer family: Genome AnalyzerIIx, HiSeq 2500, HiSeq 2000, HiSeq 1500, HiSeq 1000, Hi

  14. The Integrated Airport: Building a Successful NextGen Testbed

    SciTech Connect

    Frederick-Recascino, Christina; Sweigard, Doug; Lester, Wade

    2009-02-18

    This presentation will describe a unique public-private partnership - the Integrated Airport - that was created to engage in research and testing related to NextGen Technology deployment. NextGen refers to the program that will be initiated to modernize the US National Airspace. As with any major, multi-decade initiative, such as NextGen, integration of work efforts by multiple partners in the modernization is critical for success. This talk will focus on the development of the consortium, how the consortium plans for NextGen initiatives, the series of technology demonstrations we have produced and plans for the future of NextGen testing and implementation.

  15. The Integrated Airport: Building a Successful NextGen Testbed

    SciTech Connect

    Frederick-Recascino, Christina; Sweigard, Doug; Lester, Wade

    2009-02-18

    This presentation will describe a unique public-private partnership - the Integrated Airport - that was created to engage in research and testing related to NextGen Technology deployment.  NextGen refers to the program that will be initiated to modernize the US National Airspace.  As with any major, multi-decade initiative, such as NextGen, integration of work efforts by multiple partners in the modernization is critical for success.  This talk will focus on the development of the consortium, how the consortium plans for NextGen initiatives, the series of technology demonstrations we have produced and plans for the future of NextGen testing and implementation. 

  16. The Integrated Airport: Building a Successful NextGen Testbed

    ScienceCinema

    Frederick-Recascino, Christina [Embry-Riddle Aeronautical University, Daytona Beach, Florida, United States]; Sweigard, Doug [Lockheed Martin Corporation]; Lester, Wade [ERAU

    2010-01-08

    This presentation will describe a unique public-private partnership - the Integrated Airport - that was created to engage in research and testing related to NextGen Technology deployment.  NextGen refers to the program that will be initiated to modernize the US National Airspace.  As with any major, multi-decade initiative, such as NextGen, integration of work efforts by multiple partners in the modernization is critical for success.  This talk will focus on the development of the consortium, how the consortium plans for NextGen initiatives, the series of technology demonstrations we have produced and plans for the future of NextGen testing and implementation. 

  17. Ebola and next gen. sequencing Maisie Steinbrink

    E-print Network

    Skop, Ahna

    Ebola and next gen. sequencing Maisie Steinbrink Mikayla Simons #12;Road map 1. What is Ebola? Why does it matter? 2.Next Generation Sequencing 3. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. #12;What is Ebola? #12;Types of Ebolavirus Ebola Zaire Tai Forest

  18. Gen IV Materials Handbook Implementation Plan

    SciTech Connect

    Rittenhouse, P.; Ren, W.

    2005-03-29

    A Gen IV Materials Handbook is being developed to provide an authoritative single source of highly qualified structural materials information and materials properties data for use in design and analyses of all Generation IV Reactor Systems. The Handbook will be responsive to the needs expressed by all of the principal government, national laboratory, and private company stakeholders of Gen IV Reactor Systems. The Gen IV Materials Handbook Implementation Plan provided here addresses the purpose, rationale, attributes, and benefits of the Handbook and will detail its content, format, quality assurance, applicability, and access. Structural materials, both metallic and ceramic, for all Gen IV reactor types currently supported by the Department of Energy (DOE) will be included in the Gen IV Materials Handbook. However, initial emphasis will be on materials for the Very High Temperature Reactor (VHTR). Descriptive information (e.g., chemical composition and applicable technical specifications and codes) will be provided for each material along with an extensive presentation of mechanical and physical property data including consideration of temperature, irradiation, environment, etc. effects on properties. Access to the Gen IV Materials Handbook will be internet-based with appropriate levels of control. Information and data in the Handbook will be configured to allow search by material classes, specific materials, specific information or property class, specific property, data parameters, and individual data points identified with materials parameters, test conditions, and data source. Details on all of these as well as proposed applicability and consideration of data quality classes are provided in the Implementation Plan. Website development for the Handbook is divided into six phases including (1) detailed product analysis and specification, (2) simulation and design, (3) implementation and testing, (4) product release, (5) project/product evaluation, and (6) product maintenance and enhancement. Contracting of development of the Handbook website is discussed in terms of host server options, cost, technology, developer background and cooperative nature, and company stability. One of the first and most important activities in website development will be the generation of a detailed Handbook product requirements document including case diagrams and functional requirements tables. The Implementation Plan provides a detailed overview of the organizational structure of the Handbook and details of Handbook preparation, publication, and distribution. Finally, the Implementation Plan defines Quality Assurance requirements for the Handbook.

  19. An Gen2 Based Security Authentication Protocol for RFID System

    NASA Astrophysics Data System (ADS)

    Yi, Xiaoluo; Wang, Liangmin; Mao, Dongmei; Zhan, Yongzhao

    EPC Class-1 Generation-2 specification(Gen2 in brief) has been accepted as the standard for RFID tags under grant number ISO18000-6C. However, Gen2 does not pay due attention to security. For this reason, a Gen2 based security authentication protocol is developed in this paper. In details, we study the security requirements presented in the current Gen2 based RFID authentication protocols[7-13]. Then we point out the security flaws of Chien's mutual authentication protocol[7], and improve the protocol based on a 11 security requirements. Our improved protocol merely uses CRC and PRNG operations supported by Gen2 and meets the 11 security requirements. In contrast to the similar work [14,15] on Chien's protocol or other Gen2 based schemes, our protocol is more secure and our security analysis is much more comprehensive and qualitative.

  20. Safety Assurance in NextGen

    NASA Technical Reports Server (NTRS)

    HarrisonFleming, Cody; Spencer, Melissa; Leveson, Nancy; Wilkinson, Chris

    2012-01-01

    The generation of minimum operational, safety, performance, and interoperability requirements is an important aspect of safely integrating new NextGen components into the Communication Navigation Surveillance and Air Traffic Management (CNS/ATM) system. These requirements are used as part of the implementation and approval processes. In addition, they provide guidance to determine the levels of design assurance and performance that are needed for each element of the new NextGen procedures, including aircraft, operator, and Air Navigation and Service Provider. Using the enhanced Airborne Traffic Situational Awareness for InTrail Procedure (ATSA-ITP) as an example, this report describes some limitations of the current process used for generating safety requirements and levels of required design assurance. An alternative process is described, as well as the argument for why the alternative can generate more comprehensive requirements and greater safety assurance than the current approach.

  1. Complications Following BellaGen™ Injection

    PubMed Central

    Park, Mi Kyung; Kim, Hyun Kyu; Park, Kui Young; Li, Kapsok; Hong, Chang Kwun

    2011-01-01

    BellaGen™ is an injectable acellular dermal matrix granule derived from donated human skin tissue that was recently developed for soft tissue augmentation. Its use has been sporadically reported in penile girth enhancement procedures. Many cases of complications have been reported after injecting acellular dermal matrices like AlloDerm or SureDerm™ but few reports on complications associated with BellaGen™ injection. We report here on penile skin inflammation and necrosis following augmentation phalloplasty with BellaGen™, which developed 3 days after the injection and persisted for more than 2 weeks. The patient had a 15 year history of type 2 diabetes mellitus, and he was treated with oral antibiotics and wet dressings with KMNO4 solution to combine preservation of the remaining penile soft tissue with debridement of avascular tissue. The lesion improved with this treatment, but the patient experienced pain for about 2 weeks. All patients should be informed of the potential complications with the use of injectable acellular dermal matrices before treatment. Patient selection for augmentation is also important to have the most desirable results. PMID:22346264

  2. GEN3D Ver. 1.37

    Energy Science and Technology Software Center (ESTSC)

    2012-01-04

    GEN3D is a three-dimensional mesh generation program. The three-dimensional mesh is generated by mapping a two-dimensional mesh into threedimensions according to one of four types of transformations: translating, rotating, mapping onto a spherical surface, and mapping onto a cylindrical surface. The generated three-dimensional mesh can then be reoriented by offsetting, reflecting about an axis, and revolving about an axis. GEN3D can be used to mesh geometries that are axisymmetric or planar, but, due to three-dimensionalmore »loading or boundary conditions, require a three-dimensional finite element mesh and analysis. More importantly, it can be used to mesh complex three-dimensional geometries composed of several sections when the sections can be defined in terms of transformations of two dimensional geometries. The code GJOIN is then used to join the separate sections into a single body. GEN3D reads and writes twodimensional and threedimensional mesh databases in the GENESIS database format; therefore, it is compatible with the preprocessing, postprocessing, and analysis codes used by the Engineering Analysis Department at Sandia National Laboratories, Albuquerque, NM.« less

  3. New records of the Cryphonectriaceae from southern Africa including Latruncellus aurorae gen. sp. nov.

    E-print Network

    New records of the Cryphonectriaceae from southern Africa including Latruncellus aurorae gen. sp, Latruncellus aurorae gen. sp. nov., is described from Galpinia transvaalica (Lythraceae, Myrtales) in Swazi

  4. Towards an International Culture: Gen Y Students and SNS?

    ERIC Educational Resources Information Center

    Lichy, Jessica

    2012-01-01

    This article reports the findings of a small-scale investigation into the Internet user behaviour of generation Y (Gen Y) students, with particular reference to social networking sites. The study adds to the literature on cross-cultural Internet user behaviour with specific reference to Gen Y and social networking. It compares how a cohort of…

  5. Representation for ViewGen: Structures and Reasoning

    E-print Network

    Hartley, Roger

    in terms of the structures and reasoning mechanisms contained in the Conceptual Programming system, CP which is based on Sowa's conceptual structures. Each of the constructs in ViewGen is shown in its CP form, and the major operations, ascription and percolation are shown as CP operations. 1 ViewGen and CP

  6. DiffGen: Automated Regression Unit-Test Kunal Taneja

    E-print Network

    Xie, Tao

    DiffGen: Automated Regression Unit-Test Generation Kunal Taneja Department of Computer ScienceGen for automated regression unit-test generation and checking for Java programs. Given two versions of a Java class maintenance cost is in fact spent on regression testing. Developers need to have regression tests that can

  7. TidGen Power System Commercialization Project

    SciTech Connect

    Sauer, Christopher R.; McEntee, Jarlath

    2013-12-30

    ORPC Maine, LLC, a wholly-owned subsidiary of Ocean Renewable Power Company, LLC (collectively ORPC), submits this Final Technical Report for the TidGen® Power System Commercialization Project (Project), partially funded by the U.S. Department of Energy (DE-EE0003647). The Project was built and operated in compliance with the Federal Energy Regulatory Commission (FERC) pilot project license (P-12711) and other permits and approvals needed for the Project. This report documents the methodologies, activities and results of the various phases of the Project, including design, engineering, procurement, assembly, installation, operation, licensing, environmental monitoring, retrieval, maintenance and repair. The Project represents a significant achievement for the renewable energy portfolio of the U.S. in general, and for the U.S. marine hydrokinetic (MHK) industry in particular. The stated Project goal was to advance, demonstrate and accelerate deployment and commercialization of ORPC’s tidal-current based hydrokinetic power generation system, including the energy extraction and conversion technology, associated power electronics, and interconnection equipment capable of reliably delivering electricity to the domestic power grid. ORPC achieved this goal by designing, building and operating the TidGen® Power System in 2012 and becoming the first federally licensed hydrokinetic tidal energy project to deliver electricity to a power grid under a power purchase agreement in North America. Located in Cobscook Bay between Eastport and Lubec, Maine, the TidGen® Power System was connected to the Bangor Hydro Electric utility grid at an on-shore station in North Lubec on September 13, 2012. ORPC obtained a FERC pilot project license for the Project on February 12, 2012 and the first Maine Department of Environmental Protection General Permit issued for a tidal energy project on January 31, 2012. In addition, ORPC entered into a 20-year agreement with Bangor Hydro Electric Company on January 1, 2013 for up to 5 megawatts at a price of $215/MWh, escalating at 2.0% per year.

  8. Gen IV Materials Handbook Functionalities and Operation

    SciTech Connect

    Ren, Weiju

    2009-12-01

    This document is prepared for navigation and operation of the Gen IV Materials Handbook, with architecture description and new user access initiation instructions. Development rationale and history of the Handbook is summarized. The major development aspects, architecture, and design principles of the Handbook are briefly introduced to provide an overview of its past evolution and future prospects. Detailed instructions are given with examples for navigating the constructed Handbook components and using the main functionalities. Procedures are provided in a step-by-step fashion for Data Upload Managers to upload reports and data files, as well as for new users to initiate Handbook access.

  9. Back to the FutureGen?

    SciTech Connect

    Buchsbaum, L.

    2009-04-15

    After years of political wrangling, Democrats may green-light the experimental clean coal power plants. The article relates how the project came to be curtailed, how Senator Dick Durbin managed to protect $134 million in funding for FutureGen in Mattoon, and how once Obama was in office a $2 billion line item to fund a 'near zero emissions power plant(s)' was placed in the Senate version of the Stimulus Bill. The final version of the legislation cut the funding to $1 billion for 'fossil energy research and development'. In December 2008 the FutureGen Alliance and the City of Mattoon spent $6.5 billion to purchase the plants eventual 440 acre site. A report by the Government Accountability Office (GAO) said that Bush's inaction may have set back clean coal technology in the US by as much as a decade. If additional funding comes through construction of the plant could start in 2010. 1 fig., 1 photo.

  10. RxGen General Optical Model Prescription Generator

    NASA Technical Reports Server (NTRS)

    Sigrist, Norbert

    2012-01-01

    RxGen is a prescription generator for JPL's in-house optical modeling software package called MACOS (Modeling and Analysis for Controlled Optical Systems), which is an expert optical analysis software package focusing on modeling optics on dynamic structures, deformable optics, and controlled optics. The objectives of RxGen are to simplify and automate MACOS prescription generations, reducing errors associated with creating such optical prescriptions, and improving user efficiency without requiring MACOS proficiency. RxGen uses MATLAB (a high-level language and interactive environment developed by MathWorks) as the development and deployment platform, but RxGen can easily be ported to another optical modeling/analysis platform. Running RxGen within the modeling environment has the huge benefit that variations in optical models can be made an integral part of the modeling state. For instance, optical prescription parameters determined as external functional dependencies, optical variations by controlling the in-/exclusion of optical components like sub-systems, and/or controlling the state of all components. Combining the mentioned capabilities and flexibilities with RxGen's optical abstraction layer completely eliminates the hindering aspects for requiring proficiency in writing/editing MACOS prescriptions, allowing users to focus on the modeling aspects of optical systems, i.e., increasing productivity and efficiency. RxGen provides significant enhancements to MACOS and delivers a framework for fast prototyping as well as for developing very complex controlled optical systems.

  11. Head-Worn Displays for NextGen

    NASA Technical Reports Server (NTRS)

    Bailey, Randall E.; Shelton, Kevin J.; Arthur, J. J.

    2011-01-01

    The operating concepts emerging under the Next Generation air transportation system (NextGen) require new technology and procedures - not only on the ground-side - but also on the flight deck. Flight deck display and decision support technologies are specifically targeted to overcome aircraft safety barriers that might otherwise constrain the full realization of NextGen. One such technology is the very lightweight, unobtrusive head-worn display (HWD). HWDs with an integrated head-tracking system are being researched as they offer significant potential benefit under emerging NextGen operational concepts. Two areas of benefit for NextGen are defined. First, the HWD may be designed to be equivalent to the Head-Up Display (HUD) using Virtual HUD concepts. As such, these operational credits may be provided to significantly more aircraft for which HUD installation is neither practical nor possible. Second, the HWD provides unique display capabilities, such as an unlimited field-of-regard. These capabilities may be integral to emerging NextGen operational concepts, eliminating safety issues which might otherwise constrain the full realization of NextGen. The paper details recent research results, current HWD technology limitations, and future technology development needed to realize HWDs as a enabling technology for NextGen.

  12. Head-worn displays for NextGen

    NASA Astrophysics Data System (ADS)

    Bailey, Randall E.; Shelton, Kevin J.; Arthur, J. J., III

    2011-06-01

    The operating concepts emerging under the Next Generation air transportation system (NextGen) require new technology and procedures - not only on the ground-side - but also on the flight deck. Flight deck display and decision support technologies are specifically targeted to overcome aircraft safety barriers that might otherwise constrain the full realization of NextGen. One such technology is the very lightweight, unobtrusive head-worn display (HWD). HWDs with an integrated head-tracking system are being researched as they offer significant potential benefit under emerging NextGen operational concepts. Two areas of benefit for NextGen are defined. First, the HWD may be designed to be equivalent to the Head-Up Display (HUD) using Virtual HUD concepts. As such, these operational credits may be provided to significantly more aircraft for which HUD installation is neither practical nor possible. Second, the HWD provides unique display capabilities, such as an unlimited field-of-regard. These capabilities may be integral to emerging NextGen operational concepts, eliminating safety issues which might otherwise constrain the full realization of NextGen. The paper details recent research results, current HWD technology limitations, and future technology development needed to realize HWDs as a enabling technology for NextGen.

  13. Skryjelites auritus gen. et sp. nov. and Quasimolites quasimodo gen. et sp. nov.-two new middle Cambrian hyolithids (?Mollusca) from the Czech Republic.

    PubMed

    Valent, Martin; Fatka, Old?ich; Szabad, Michal; Micka, Václav; Marek, Ladislav

    2015-01-01

    Two new endemic genera and species of extinct group of Hyolitha, Skryjelites auritus gen. et sp. nov. and Quasimolites quasimodo gen. et sp. nov. are described and illustrated from the Buchava Formation of the Barrandian area (Czech Republic). PMID:26623820

  14. NextGen Future Safety Assessment Game

    NASA Technical Reports Server (NTRS)

    Ancel, Ersin; Gheorghe, Adian; Jones, Sharon Monica

    2010-01-01

    The successful implementation of the next generation infrastructure systems requires solid understanding of their technical, social, political and economic aspects along with their interactions. The lack of historical data that relate to the long-term planning of complex systems introduces unique challenges for decision makers and involved stakeholders which in turn result in unsustainable systems. Also, the need to understand the infrastructure at the societal level and capture the interaction between multiple stakeholders becomes important. This paper proposes a methodology in order to develop a holistic approach aiming to provide an alternative subject-matter expert (SME) elicitation and data collection method for future sociotechnical systems. The methodology is adapted to Next Generation Air Transportation System (NextGen) decision making environment in order to demonstrate the benefits of this holistic approach.

  15. 1. GENERAL VIEW. Statues: Maj. Gen George Meade by Daniel ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. GENERAL VIEW. Statues: Maj. Gen George Meade by Daniel Chester French, south side; Maj. Gen. John Reynolds by Charles Grafly, north side. Equestrian Statues: Maj. Gen George B. McClellan by Edward C. Potter, south side; Maj. Gen Winfield S. Hancock by J.Q.A. Ward, north side. The statue at the base of northern inner pedestal is Richard Smith, a type founder and donor of the Memorial. The niches are filled with eight colossal busts including Union generals, admirals, Pennsylvania governor, Memorial's architects (John T. and James H. Windrim), and executor of Smith's will. The frieze is carved with the names of eighty-four prominent Pennsylvania participants in the Civil War. - Smith Memorial Arch, Philadelphia, Philadelphia County, PA

  16. Sources of data in the GenBank database

    SciTech Connect

    Burks, C.

    1987-01-01

    The citations in GenBank are characterized with respect to form of publication. The potential spectrum of quality control problems applicable to the various types of unpublished data are discussed. 6 refs., 2 tabs.

  17. 78 FR 8108 - NextGen Solutions Vendors Guide

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-05

    ... participating in the NextGen Solutions Vendors Guide by post or email to the attention of Jonathan Alvear... using ADS-B (d) Efficient flight paths Example: Trajectory-Based Operations--Improved Safety...

  18. 75 FR 5780 - Green Borders Geothermal, LLC, Complainant, v. Terra-Gen Dixie Valley, LLC, Respondent; Notice of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-04

    ...Geothermal, LLC, Complainant, v. Terra-Gen Dixie Valley, LLC, Respondent...Borders) filed a formal complaint against Terra-Gen Dixie Valley, LLC (f/k/a Caithness Dixie Valley, LLC) (Terra-Gen) pursuant to section 206 of...

  19. GWAS in a Box: Statistical and Visual Analytics of Structured Associations via GenAMap

    E-print Network

    Murphy, Robert F.

    1 GWAS in a Box: Statistical and Visual Analytics of Structured Associations via GenAMap Eric P. Algorithmically, GenAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association

  20. Parachloroidium gen. nov. (Trebouxiophyceae, Chlorophyta), a novel genus of coccoid green algae from subaerial corticolous biofilms

    E-print Network

    Parachloroidium gen. nov. (Trebouxiophyceae, Chlorophyta), a novel genus of coccoid green algae. Parachloroidium gen. nov. (Trebouxiophyceae, Chlorophyta), a novel genus of coccoid green algae from subaerial the Parachloroidium strains from other similar green algae. However, ultrastructural characteristics and molecular

  1. A Virtual Reality Framework to Optimize Design, Operation and Refueling of GEN-IV Reactors.

    SciTech Connect

    Rizwan-uddin; Nick Karancevic; Stefano Markidis; Joel Dixon; Cheng Luo; Jared Reynolds

    2008-04-23

    many GEN-IV candidate designs are currently under investigation. Technical issues related to material, safety and economics are being addressed at research laboratories, industry and in academia. After safety, economic feasibility is likely to be the most important crterion in the success of GEN-IV design(s). Lessons learned from the designers and operators of GEN-II (and GEN-III) reactors must play a vital role in achieving both safety and economic feasibility goals.

  2. Genes and proteins of Escherichia coli (GenProtEc).

    PubMed

    Riley, M; Space, D B

    1996-01-01

    GenProtEc is a database of Escherichia coli genes and their gene products, classified by type of function and physiological role and with citations to the literature for each. Also present are data on sequence similarities among E.coli proteins with PAM values, percent identity of amino acids, length of alignment and percent aligned. The database is available as a PKZip file by ftp from mbl.edu/pub/ecoli.exe. The program runs under MS-DOS on IMB-compatible machines. GenProtEc can also be accessed through the World Wide Web at URL http://mbl.edu/html/ecoli.html. PMID:8594596

  3. DOE/NNSA perspective safeguard by design: GEN III/III+ light water reactors and beyond

    SciTech Connect

    Pan, Paul Y

    2010-12-10

    An overview of key issues relevant to safeguards by design (SBD) for GEN III/IV nuclear reactors is provided. Lessons learned from construction of typical GEN III+ water reactors with respect to SBD are highlighted. Details of SBD for safeguards guidance development for GEN III/III+ light water reactors are developed and reported. This paper also identifies technical challenges to extend SBD including proliferation resistance methodologies to other GEN III/III+ reactors (except HWRs) and GEN IV reactors because of their immaturity in designs.

  4. GenAnneal: Genetically modified Simulated Annealing

    NASA Astrophysics Data System (ADS)

    Tsoulos, Ioannis G.; Lagaris, Isaac E.

    2006-05-01

    A modification of the standard Simulated Annealing (SA) algorithm is presented for finding the global minimum of a continuous multidimensional, multimodal function. We report results of computational experiments with a set of test functions and we compare to methods of similar structure. The accompanying software accepts objective functions coded both in Fortran 77 and C++. Program summaryTitle of program:GenAnneal Catalogue identifier:ADXI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXI_v1_0 Program available from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: The tool is designed to be portable in all systems running the GNU C++ compiler Installation: University of Ioannina, Greece on Linux based machines Programming language used:GNU-C++, GNU-C, GNU Fortran 77 Memory required to execute with typical data: 200 KB No. of bits in a word: 32 No. of processors used: 1 Has the code been vectorized or parallelized?: No No. of bytes in distributed program, including test data, etc.:84 885 No. of lines in distributed program, including test data, etc.:14 896 Distribution format: tar.gz Nature of physical problem: A multitude of problems in science and engineering are often reduced to minimizing a function of many variables. There are instances that a local optimum does not correspond to the desired physical solution and hence the search for a better solution is required. Local optimization techniques are frequently trapped in local minima. Global optimization is hence the appropriate tool. For example, solving a non-linear system of equations via optimization, employing a "least squares" type of objective, one may encounter many local minima that do not correspond to solutions (i.e. they are far from zero). Typical running time: Depending on the objective function. Method of solution: We modified the process of step selection that the traditional Simulated Annealing employs and instead we used a global technique based on grammatical evolution.

  5. Biogas Purification Process to Increase Gen—Set Efficiency

    NASA Astrophysics Data System (ADS)

    Krido Wahono, Satriyo; Maryana, Roni; Kismurtono, M.

    2009-09-01

    Because of global issue about limited energy, biogas was one of alternative energy and save energy in the world which produced from biomass especially from cow manure. Most of biogas which produced from cow manure contains 40-75% methane as energy resources and another gas as impurities. Methane concentration of biogas has relation with biogas energy value, especially for application as fuel of electricity conversion using gen-set. For increasing gen-set efficiency can be held by increasing methane concentration of biogas using biogas purification process. Biogas purification process can be held by adsorption system which using activated zeolite as absorber. After biogas through the purification system, methane concentration was increasing and impacting to gen-set efficiency especially voltage value was increasing until 22 times in average better than without purification and keeping power stability, so it will produce electricity conversion until 39,07% of practical and 38,09% of equation calculation from maximum electric power output of gen-set.

  6. Secure EPC Gen2 compliant Radio Frequency Identification

    E-print Network

    International Association for Cryptologic Research (IACR)

    Introduction Radio Frequency Identification (RFID) is a promising new technology that is widely deployedSecure EPC Gen2 compliant Radio Frequency Identification Mike Burmester1 , Breno de Medeiros2) is making this standard a de facto specification for inexpensive tags in the RFID industry. Recently three

  7. November 2015 Edition GenCen News and Events

    E-print Network

    DIGEST November 2015 Edition -- GenCen News and Events Please bear with us as we experience ongoing Learning and Leadership Training. Web Course; Workshops. November 18, December 1 Muslim Journeys Book Club investigations as government report released se bear with us as we experience ongoing website issues

  8. Competitive Learning for Deep Temporal Networks Robert Gens

    E-print Network

    Anderson, Richard

    Competitive Learning for Deep Temporal Networks Robert Gens Computer Science and Engineering of competitive learning in deep networks for understanding sequential data. Hierarchies of competitive learning algorithms have been found in the brain [1] and their use in deep vision networks has been validated [2

  9. A New Parent Generation: Meet Mr. and Mrs. Gen X

    ERIC Educational Resources Information Center

    Howe, Neil

    2010-01-01

    Slowly but surely, Generation Xers have been taking over from Baby Boomers as the majority of parents in elementary and secondary education. Gen-X parents and Boomer parents belong to two neighboring generations, each possessing its own location in history and its own peer personality. They are similar in some respects, but clearly different in…

  10. Meet Mr. and Mrs. Gen X: A New Parent Generation

    ERIC Educational Resources Information Center

    Howe, Neil

    2010-01-01

    Slowly but surely, Generation Xers have been taking over from Baby Boomers as the majority of parents in elementary and secondary education. In the early 1990s, Gen Xers began joining parent-teacher associations in the nation's elementary schools. Around 2005, they became the majority of middle school parents. By the fall of 2008, they took over…

  11. Safer Systems: A NextGen Aviation Safety Strategic Goal

    NASA Technical Reports Server (NTRS)

    Darr, Stephen T.; Ricks, Wendell R.; Lemos, Katherine A.

    2008-01-01

    The Joint Planning and Development Office (JPDO), is charged by Congress with developing the concepts and plans for the Next Generation Air Transportation System (NextGen). The National Aviation Safety Strategic Plan (NASSP), developed by the Safety Working Group of the JPDO, focuses on establishing the goals, objectives, and strategies needed to realize the safety objectives of the NextGen Integrated Plan. The three goal areas of the NASSP are Safer Practices, Safer Systems, and Safer Worldwide. Safer Practices emphasizes an integrated, systematic approach to safety risk management through implementation of formalized Safety Management Systems (SMS) that incorporate safety data analysis processes, and the enhancement of methods for ensuring safety is an inherent characteristic of NextGen. Safer Systems emphasizes implementation of safety-enhancing technologies, which will improve safety for human-centered interfaces and enhance the safety of airborne and ground-based systems. Safer Worldwide encourages coordinating the adoption of the safer practices and safer systems technologies, policies and procedures worldwide, such that the maximum level of safety is achieved across air transportation system boundaries. This paper introduces the NASSP and its development, and focuses on the Safer Systems elements of the NASSP, which incorporates three objectives for NextGen systems: 1) provide risk reducing system interfaces, 2) provide safety enhancements for airborne systems, and 3) provide safety enhancements for ground-based systems. The goal of this paper is to expose avionics and air traffic management system developers to NASSP objectives and Safer Systems strategies.

  12. Fossil energy, clean coal technology, and FutureGen

    SciTech Connect

    Sarkus, T.A.

    2008-07-15

    Future fossil use will rely heavily on carbon sequestration. Clean coal technologies are being incorporated in the USA, including air pollution control, and will need to incorporate carbon capture and sequestration. The paper ends with an outline of the restructured FutureGen project. 7 figs.

  13. AnoGen: A Program for Generating ANOVA Data Sets.

    ERIC Educational Resources Information Center

    Miller, Jeff

    1999-01-01

    Describes a computer program called AnoGen that automates the process of generating data sets for ANOVA designs and operates within DOS and Windows compatible computers. Explains that the program runs in both student and teacher modes and is freely available for noncommercial use through the Internet. (CMK)

  14. Recommended Academic Plan Biotechnology General Option (BIOTC Gen at UP)

    E-print Network

    Babu, G. Jogesh

    Recommended Academic Plan Biotechnology General Option (BIOTC Gen at UP) Effective Fall 2012 Biochemistry 2 MICRB 410 Principles of Immunology 3 BIOTC 459 Plant Tissue Culture & Biotechnology 3 MICRB 421W BIOTC 416 Microbial Biotechnology 2 Arts (GA), Humanities (GH) or Social Behavioral Sciences (GS) 3 Arts

  15. Advanced Vehicle Concepts and Implications for NextGen

    NASA Technical Reports Server (NTRS)

    Blake, Matt; Smith, Jim; Wright, Ken; Mediavilla Ricky; Kirby, Michelle; Pfaender, Holger; Clarke, John-Paul; Volovoi, Vitali; Dorbian, Christopher; Ashok, Akshay; Reynolds, Tom; Waitz, Ian; Hileman, James; Arunachalam, Sarav; Hedrick, Matt; Vempati, Lakshmi; Laroza, Ryan; denBraven, Wim; Henderson, Jeff

    2010-01-01

    This report presents the results of a major NASA study of advanced vehicle concepts and their implications for the Next Generation Air Transportation System (NextGen). Comprising the efforts of dozens of researchers at multiple institutions, the analyses presented here cover a broad range of topics including business-case development, vehicle design, avionics, procedure design, delay, safety, environmental impacts, and metrics. The study focuses on the following five new vehicle types: Cruise-efficient short takeoff and landing (CESTOL) vehicles Large commercial tiltrotor aircraft (LCTRs) Unmanned aircraft systems (UAS) Very light jets (VLJs) Supersonic transports (SST). The timeframe of the study spans the years 2025-2040, although some analyses are also presented for a 3X scenario that has roughly three times the number of flights as today. Full implementation of NextGen is assumed.

  16. Radio Transmission Performance of EPCglobal Gen-2 RFID System

    E-print Network

    Mohaisen, Manar; Chang, KyungHi

    2009-01-01

    In this paper, we analyze the performance of the encoding and the modulation processes in the downlink and uplink of the EPCglobal Gen2 system through the analysis and simulation. Furthermore, the synchronization issues on time and frequency domain and the preamble architecture are evaluated. Through the simulation in the uplink, we find that the detection probability of FM0 and Miller coding approaches 1 at 13dB Eb/N0.

  17. Universite de Gen`eve Automne 2009 Section de Mathematiques

    E-print Network

    Audoux, Benjamin

    Universit´e de Gen`eve Automne 2009 Section de Math´ematiques G´eom´etrie II Consignes Consignes 623, au 6`eme ´etage de la section de math´ematiques. Tous les mercredi matin, le professeur'est ainsi que l'on apprend les math´ematiques. Coordonn´ees : Professeur : Andr´as Szenes Bureau 11, 2`eme

  18. GEN IV reactors: Where we are, where we should go

    SciTech Connect

    Locatelli, G.; Mancini, M.; Todeschini, N.

    2012-07-01

    GEN IV power plants represent the mid-long term option of the nuclear sector. International literature proposes many papers and reports dealing with these reactors, but there is an evident difference of type and shape of information making impossible each kind of detailed comparison. Moreover, authors are often strongly involved in some particular design; this creates many difficulties in their super-partes position. Therefore it is necessary to put order in the most relevant information to understand strengths and weaknesses of each design and derive an overview useful for technicians and policy makers. This paper presents the state-of the art for GEN IV nuclear reactors providing a comprehensive literature review of the different designs with a relate taxonomy. It presents the more relevant references, data, advantages, disadvantages and barriers to the adoptions. In order to promote an efficient and wide adoption of GEN IV reactors the paper provides the pre-conditions that must be accomplished, enabling factors promoting the implementation and barriers limiting the extent and intensity of its implementation. It concludes outlying the state of the art of the most important R and D areas and the future achievements that must be accomplished for a wide adoption of these technologies. (authors)

  19. Pantanalinema gen. nov. and Alkalinema gen. nov.: novel pseudanabaenacean genera (Cyanobacteria) isolated from saline-alkaline lakes.

    PubMed

    Vieira Vaz, Marcelo Gomes Marçal; Genuário, Diego Bonaldo; Andreote, Ana Paula Dini; Malone, Camila Francieli Silva; Sant'Anna, Célia Leite; Barbiero, Laurent; Fiore, Marli Fátima

    2015-01-01

    The genus Leptolyngbya Anagnostidis & Komárek (1988) was described from a set of strains identified as 'LPP-group B'. The morphology within this group is not particularly informative and underestimates the group's genetic diversity. In the present study, two new pseudanabaenacean genera related to Leptolyngbya morphotypes, Pantanalinema gen. nov. and Alkalinema gen. nov., are described under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants, based on a polyphasic approach. Pantanalinema gen. nov. (type species Pantanalinema rosaneae sp. nov.) has sheaths and trichomes with slight gliding motility, which distinguish this genus from Alkalinema gen. nov. (type species Alkalinema pantanalense sp. nov.), which possesses trichomes arranged in an ornate (interwoven) pattern. 16S rRNA gene sequences of strains of Pantanalinema and Alkalinema exhibited low identity to each other (?91.6?%) and to other sequences from known pseudanabaenacean genera (?94.3 and 93.7?%, respectively). In a phylogenetic reconstruction, six sequences from strains of Pantanalinema and four from strains of Alkalinema formed two separate and robust clades (99?% bootstrap value), with the genera Oculatella and Phormidesmis, respectively, as the closest related groups. 16S-23S rRNA intergenic spacer sequences and secondary structures of strains of Pantanalinema and Alkalinema did not correspond to any previous descriptions. The strains of Pantanalinema and Alkalinema were able to survive and produce biomass at a range of pH (pH 4-11) and were also able to alter the culture medium to pH values ranging from pH 8.4 to 9.9. These data indicate that cyanobacterial communities in underexplored environments, such as the Pantanal wetlands, are promising sources of novel taxa. PMID:25351877

  20. VitisGen on the road: mapping the way to the next generation of grapes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA-NIFA VitisGen project (Award No. 2011-51181-30635) aims to optimize grape cultivar improvement through the integration of grape breeding, cutting edge genomics technology, precision phenotyping, socioeconomic research, and extension. VitisGen is a five-year project involving 25 co-PIs at 11...

  1. USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 879 Water, Wildlife, Recreation, Timber...

    E-print Network

    in the central Sierra Nevada. After 20 years of harvesting timber and using prescribed burns, I have determined Woody Debris?--Mount USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002.880 property, and at the sameUSDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 879 Water, Wildlife, Recreation, Timber

  2. Modelling Departure Time Choices by a Heteroskedastic Generalized Logit (Het-GenL) Model

    E-print Network

    Toronto, University of

    Modelling Departure Time Choices by a Heteroskedastic Generalized Logit (Het-GenL) Model 2012 #12;1 Modelling Departure Time Choices by a Heteroskedastic Generalized Logit (Het-GenL) Model.nurulhabib@utoronto.ca Abstract The paper presents an econometric model for departure time choice modelling. The proposed model

  3. 76 FR 28973 - Terra-Gen Dixie Valley, LLC; Order on Rehearing and Accepting Tariff Filing, Subject to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-19

    ...ER11-2127-001, ER11-2127-002, EL11-37-000] Terra-Gen Dixie Valley, LLC; Order on Rehearing and...access transmission tariff (OATT) submitted by Terra-Gen Dixie Valley, LLC (Terra-Gen), in response to a Commission order...

  4. Spatial control of the GEN1 Holliday junction resolvase ensures genome stability

    PubMed Central

    Chan, Ying Wai; West, Stephen C.

    2014-01-01

    Holliday junction (HJ) resolvases are necessary for the processing of persistent recombination intermediates before cell division. Their actions, however, need to be restricted to the late stages of the cell cycle to avoid the inappropriate cleavage of replication intermediates. Control of the yeast HJ resolvase, Yen1, involves phosphorylation changes that modulate its catalytic activity and nuclear import. Here, we show that GEN1, the human ortholog of Yen1, is regulated by a different mechanism that is independent of phosphorylation. GEN1 is controlled exclusively by nuclear exclusion, driven by a nuclear export signal (NES) that restricts GEN1 actions to mitosis when the nuclear membrane breaks down. Construction of a nuclear-localized version of GEN1 revealed that its premature actions partially suppress phenotypes associated with loss of BLM and MUS81, but cause elevated crossover formation. The spatial control of GEN1 therefore contributes to genome stability, by avoiding competition with non-crossover promoting repair pathways. PMID:25209024

  5. Frigitilla gen. nov., a new genus of Amazonian Mutillidae (Hymenoptera).

    PubMed

    Bartholomay, Pedro R; Williams, Kevin A; Luz, David R; Morato, Elder F

    2015-01-01

    Mutilla frigidula Cresson, 1902 was transferred to Tobantilla by Williams et al. (2011), based on morphological similarities with females of that genus. Discovery of the male of this species indicated significant morphological differences from Tobantilla. We therefore erect the genus, Frigitilla gen. nov., for Mutilla frigidula. Herein, we describe the male of F. frigidula (Cresson, 1902), comb. nov., associate it with its host (Trypoxylon spp.), and discuss its relations to other mutillid genera. The impact of collecting method and specimen age on the integumental coloration of specimens is discussed, emphasizing the need to diagnose species on consistent structural features rather than differences in color pattern. PMID:26249052

  6. Hunting for new restriction enzymes in GenBank

    SciTech Connect

    Roberts, R.J.

    1997-12-01

    Restriction enzyme genes are hard to identify unless their surrounding sequences are available. This is because the best definition of a restriction enzyme gene is an open reading frame, that looks like nothing else in GenBank, but lies close to a DNA methylase gene. There are other clues too, such as nearby reading frames that code control proteins or the DNA specificity subunits of Type I restriction enzymes. We are developing software that searches the daily updates of GenBank to find candidate restriction enzyme genes. This is being followed by bench experiments to see of the predictions are correct. More than 50 potential new restriction enzymes have been predicted and it is quite remarkable that the density of restriction enzyme genes in microbial DNA is greater than one system per 200 Kb. The software development is emphasizing the graphic presentation of the search results. The approach could be used for other situations where a molecular biologist is interested to find new examples of their favorite genes.

  7. Mutation and association analysis of GEN1 in breast cancer susceptibility.

    PubMed

    Turnbull, Clare; Hines, Sarah; Renwick, Anthony; Hughes, Deborah; Pernet, David; Elliott, Anna; Seal, Sheila; Warren-Perry, Margaret; Gareth Evans, D; Eccles, Diana; Stratton, Michael R; Rahman, Nazneen

    2010-11-01

    GEN1 was recently identified as a key Holliday junction resolvase involved in homologous recombination. Somatic truncating GEN1 mutations have been reported in two breast cancers. Together these data led to the proposition that GEN1 is a breast cancer predisposition gene. In this article we have formally investigated this hypothesis. We performed full-gene mutational analysis of GEN1 in 176 BRCA1/2-negative familial breast cancer samples and 159 controls. We genotyped six SNPs tagging the 30 common variants in the transcribed region of GEN1 in 3,750 breast cancer cases and 4,907 controls. Mutation analysis revealed one truncating variant, c.2515_2519delAAGTT, which was present in 4% of cases and 4% of controls. We identified control individuals homozygous for the deletion, demonstrating that the last 69 amino acids of GEN1 are dispensable for its function. We identified 17 other variants, but their frequency did not significantly differ between cases and controls. Analysis of 3,750 breast cancer cases and 4,907 controls demonstrated no evidence of significant association with breast cancer for six SNPs tagging the 30 common GEN1 variants. These data indicate that although it also plays a key role in double-strand DNA break repair, GEN1 does not make an appreciable contribution to breast cancer susceptibility by acting as a high- or intermediate-penetrance breast cancer predisposition gene like BRCA1, BRCA2, CHEK2, ATM, BRIP1 and PALB2 and that common GEN1 variants do not act as low-penetrance susceptibility alleles analogous to SNPs in FGFR2. Furthermore, our analyses demonstrate the importance of undertaking appropriate genetic investigations, typically full gene screening in cases and controls together with large-scale case-control association analyses, to evaluate the contribution of genes to cancer susceptibility. PMID:20512659

  8. What Can a Historian Do with AstroGen?

    NASA Astrophysics Data System (ADS)

    Tenn, Joseph S.

    2015-01-01

    "Astrogen", the Astronomy Genealogy Project, is in the development stage. Patterned after the Mathematics Genealogy Project at http://genealogy.math.ndsu.nodak.edu, it will eventually include most of the world's astronomers, past and present, and provide information about their years of life, highest degrees, universities, and thesis titles. There will also be links to online theses, home pages, and obituaries when these are available. Although a few details remain to be worked out before it becomes public, it is possible to make some use of what has already been compiled. I will give an example, comparing graduates of Harvard University, the University of California at Berkeley, and the University of Chicago from different decades, with information about their professional careers and publication records. The author welcomes queries about AstroGen and is seeking more participants.

  9. Decay heat removal in GEN IV gas cooled fast reactors.

    SciTech Connect

    Cheng, L. Y.; Wei, T. Y. C.

    2009-08-01

    The safety goal of the current designs of advanced high-temperature thermal gas-cooled reactors (HTRs) is that no core meltdown would occur in a depressurization event with a combination of concurrent safety system failures. This study focused on the analysis of passive decay heat removal (DHR) in a GEN IV direct-cycle gas-cooled fast reactor (GFR) which is based on the technology developments of the HTRs. Given the different criteria and design characteristics of the GFR, an approach different from that taken for the HTRs for passive DHR would have to be explored. Different design options based on maintaining core flow were evaluated by performing transient analysis of a depressurization accident using the system code RELAP5-3D. The study also reviewed the conceptual design of autonomous systems for shutdown decay heat removal and recommends that future work in this area should be focused on the potential for Brayton cycle DHRs.

  10. Hybrid Communication Protocols and Control Algorithms for NextGen Aircraft Arrivals

    E-print Network

    Park, Pangun

    Capacity constraints imposed by current air traffic management technologies and protocols could severely limit the performance of the Next Generation Air Transportation System (NextGen). A fundamental design decision in ...

  11. A new rhizangiid genus from the Miocene of North America (Sclerangia n. gen.; Florida, USA)

    E-print Network

    Baron-Szabo, Rosemarie; Cairns, Stephen D.

    2015-04-30

    The colonial rhizangiid genus Sclerangia n. gen. is described from the Miocene of the USA (Chipola Formation, Florida). The new genus is characterized by plocoid to subcerioid polyp integration, cylindrical to subcylindrical ...

  12. Taxonomy, phylogeny, and paleoecology of Eoseira wilsonii gen. et sp. nov., a Middle Eocene diatom

    E-print Network

    Wolfe, Alexander P.

    Taxonomy, phylogeny, and paleoecology of Eoseira wilsonii gen. et sp. nov., a Middle Eocene diatom in western North America. Fur- thermore, paleoecological inferences based on Eoseira life strategy pertain

  13. GenBrick – A Rapid Multi-Part Assembly Method for BioBricks

    E-print Network

    Gasi?nait?, Lina

    2013-10-04

    This BioBricks Foundation Request for Comments (BBF RFC) describes a novel approach, GenBrick, for the rapid assembly of multiple BioBrick RFC10-compatible parts in a single reaction, with completely flexible part order, ...

  14. Genes and proteins of Escherichia coli K-12 (GenProtEC).

    PubMed

    Riley, M

    1997-01-01

    GenProtEC is a database of Escherichia coli genes and their gene products, classified by type of function and physiological role and with citations to the literature for each. Also present are data on sequence similarities amongE.coliproteins with PAM values, percent identity of amino acids, length of alignment and percent aligned. GenProtEC can also be accessed through the World Wide Web at URL http://mbl.edu/html/ecoli.html . PMID:9016503

  15. Preliminary Investigation of Civil Tiltrotor in NextGen Airspace

    NASA Technical Reports Server (NTRS)

    Young, Larry A.; Salvano, Dan; Wright, Ken; Chung, William; Young, Ray; Miller, David; Paris, Alfanso; Gao, Huina; Cheng, Victor

    2010-01-01

    Presentation intro: Tiltrotor aircraft have long been envisioned as being a potentially viable means of commercial aviation transport. Preliminary results from an ongoing study into the operational and technological considerations of Civil Tiltrotor (CTR) operation in the Next Generation airspace, circa the 2025 time-frame, are presented and discussed. In particular, a fleet of CTR aircraft has been conceptually designed. The performance characteristics of this CTR fleet was subsequently translated into BADA (Base of Aircraft DAta) models that could be used as input to emulate CTR aircraft operations in the ACES and AvTerminal airspace and terminal area simulation tools. A network of nine North-Eastern corridor airports is the focus of the airspace simulation effort; the results from this airport network viII then be extrapolated to provide insights into systemic impact of CTRs on the National Airspace System (NAS). Future work will also be detailed as to attempts to model the systemic effects of noise and emissions from this fleet of new aircraft as well as assess their leveraged impact on public service missions, in time of need, such as major regional/national disaster relief efforts. The ideal outcome of this study is a set of results whereby Next Gen airspace CONOPs can be refined to reflect potential CTR capabilities and, conversely, CTR technology development efforts can be better informed as to key performance requirement thresholds needed to be met in order to successfully introduce these aircraft into civilian aviation operation.

  16. Youhaiella tibetensis gen. nov., sp. nov., isolated from subsurface sediment.

    PubMed

    Wang, Yun-xiang; Huang, Fa-qi; Nogi, Yuichi; Pang, Shou-Ji; Wang, Ping-kang; Lv, Jie

    2015-07-01

    A Gram-reaction-negative bacterial strain, designated fig4(T), was isolated from a subsurface sediment core of Qiangtang Basin permafrost in China. Cells were catalase- and oxidase-positive and rods. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain fig4(T )was a member of the family Hyphomicrobiaceae and was most closely related to members of the genera Pelagibacterium, Vasilyevaea and Devosia with 93.8-96.2% sequence similarities. The major cellular fatty acids were C16 : 0, C18 : 0, 11-methyl C18 : 1 ?7c, C19 : 0 cyclo ?8c and summed feature 8 (C18 : 1?7c and/or C18 : 1?6c). The major respiratory quinone was Q-10 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The DNA G+C content was 60.7 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain fig4(T) is considered to represent a novel species of a new genus in the family Hyphomicrobiaceae, for which the name Youhaiella tibetensis gen. nov., sp. nov. is proposed. The type strain is fig4(T) (?=?CGMCC 1.12719(T) = JCM 19854(T)). PMID:25829329

  17. Safety Sufficiency for NextGen: Assessment of Selected Existing Safety Methods, Tools, Processes, and Regulations

    NASA Technical Reports Server (NTRS)

    Xu, Xidong; Ulrey, Mike L.; Brown, John A.; Mast, James; Lapis, Mary B.

    2013-01-01

    NextGen is a complex socio-technical system and, in many ways, it is expected to be more complex than the current system. It is vital to assess the safety impact of the NextGen elements (technologies, systems, and procedures) in a rigorous and systematic way and to ensure that they do not compromise safety. In this study, the NextGen elements in the form of Operational Improvements (OIs), Enablers, Research Activities, Development Activities, and Policy Issues were identified. The overall hazard situation in NextGen was outlined; a high-level hazard analysis was conducted with respect to multiple elements in a representative NextGen OI known as OI-0349 (Automation Support for Separation Management); and the hazards resulting from the highly dynamic complexity involved in an OI-0349 scenario were illustrated. A selected but representative set of the existing safety methods, tools, processes, and regulations was then reviewed and analyzed regarding whether they are sufficient to assess safety in the elements of that OI and ensure that safety will not be compromised and whether they might incur intolerably high costs.

  18. Initial Investigation of Operational Concept Elements for NASA's NextGen-Airportal Project Research

    NASA Technical Reports Server (NTRS)

    Lohr, Gary; Lee, Jonathan; Poage, James L.; Tobias, Leonard

    2009-01-01

    The NextGen-Airportal Project is organized into three research focus areas: Safe and Efficient Surface Operations, Coordinated Arrival/Departure Operations Management, and Airportal Transition and Integration Management. The content in this document was derived from an examination of constraints and problems at airports for accommodating future increases in air traffic, and from an examination of capabilities envisioned for NextGen. The concepts are organized around categories of constraints and problems and therefore do not precisely match, but generally reflect, the research focus areas. The concepts provide a framework for defining and coordinating research activities that are, and will be, conducted by the NextGen-Airportal Project. The concepts will help the research activities function as an integrated set focused on future needs for airport operations and will aid aligning the research activities with NextGen key capabilities. The concepts are presented as concept elements with more detailed sub-elements under each concept element. For each concept element, the following topics are discussed: constraints and problems being addressed, benefit descriptions, required technology and infrastructure, and an initial list of potential research topics. Concept content will be updated and more detail added as the research progresses. The concepts are focused on enhancing airportal capacity and efficiency in a timeframe 20 to 25 years in the future, which is similar to NextGen's timeframe.

  19. 77 FR 56839 - GenOn Marsh Landing, LLC; Supplemental Notice That Initial Market-Based Rate Filing Includes...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-14

    ... From the Federal Register Online via the Government Printing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission GenOn Marsh Landing, LLC; Supplemental Notice That Initial Market-Based Rate...-referenced proceeding, of GenOn Marsh Landing, LLC's application for market-based rate authority, with...

  20. Complete cDNAs from Nylanderia cf. pubens (Hymenoptera: Formicidae). --GenBank accession numbers: JF815100-JF815104

    Technology Transfer Automated Retrieval System (TEKTRAN)

    5 new gene sequences were identified from workers of Caribbean crazy ant, Nylanderia cf. pubens, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are JF815100-JF815104. This information will provide scientists with genetic tools to study the popu...

  1. Complete cDNAs from Solenopsis invicta (Hymenoptera: Formicidae). --GenBank accession numbers: HM130684-HM130685.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    2 new gene sequences were identified from workers of Solenopsis invicta, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are HM130684-HM130685. This information will provide scientists with genetic tools to study the populations of this ant....

  2. Complete cDNAs from Brachymyrmex patagonicus (Hymenoptera: Formicidae). --GenBank accession numbers: GU582126-GU582140.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    15 new gene sequences were identified from workers of Brachymyrmex patagonicus, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are GU582126-GU582140. This information will provide scientists with genetic tools to study the development and the p...

  3. A Rapid Micro Polymerase Chain Reaction System (GenSpector Micro PCR) for Hepatitis B Virus DNA Detection

    E-print Network

    Oh, Kwang W.

    A Rapid Micro Polymerase Chain Reaction System (GenSpector® Micro PCR) for Hepatitis B Virus DNA reaction) system (GenSpector® Micro PCR) for the application of Hepatitis B virus (HBV) DNA detection of Hepatitis B virus (HBV) DNA detection [1]. Silicon micromachining technology has been utilized

  4. 75 FR 1052 - Terra-Gen Dixie Valley, LLC; TGP Dixie Development Company, LLC; New York Canyon, LLC; Notice of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-08

    ...Energy Regulatory Commission [Docket No. EL10-29-000] Terra-Gen Dixie Valley, LLC; TGP Dixie Development Company, LLC...December 30, 2009. Take notice that on December 24, 2009, Terra-Gen Dixie Valley, LLC, TGP Dixie Development Company,...

  5. 78 FR 56263 - HydroGen Corp., QueryObject Systems Corp., Security Intelligence Technologies, Inc., Skins, Inc...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-12

    ...SECURITIES AND EXCHANGE COMMISSION [File No. 500-1] HydroGen Corp., QueryObject Systems Corp., Security Intelligence...current and accurate information concerning the securities of HydroGen Corp. because it has not filed any periodic reports...

  6. 43USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. The Role of the California Department

    E-print Network

    43USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. The Role of the California Department was subjectedtotechnicalpeerreview; theyweretheviewsofthepresent- ers, in behalf of the organizations they represented. 2Division, Sacramento, CA 95814. #12;44 USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Mansfield Rol

  7. SQLUnitGen: SQL Injection Testing Using Static and Dynamic Analysis Yonghee Shin Laurie Williams Tao Xie

    E-print Network

    Xie, Tao

    SQLUnitGen: SQL Injection Testing Using Static and Dynamic Analysis Yonghee Shin Laurie Williams implemented a prototype of a SQL injection vulnerability detection tool, SQLUnitGen, which we compared in 2002-6 were input manipulation vulnerabilities, such as SQL injection, cross site scripting (XSS

  8. 78 FR 77670 - AlphaGen Power LLC; Supplemental Notice That Initial Market-Based Rate Filing Includes Request...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-24

    ... From the Federal Register Online via the Government Printing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission AlphaGen Power LLC; Supplemental Notice That Initial Market-Based Rate...-referenced proceeding, of AlphaGen Power LLC's application for market-based rate authority, with...

  9. Complete cDNAs from Nylanderia sp. nr. pubens (Hymenoptera: Formicidae). GenBank GU980916-GU980928.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    13 new gene sequences were identified from workers of Rasberry crazy ant, Nylanderia sp.nr. pubens, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are GU980916-GU980928. This information will provide scientists with genetic tools to study the p...

  10. 75 FR 1052 - Terra-Gen Dixie Valley, LLC; TGP Dixie Development Company, LLC; New York Canyon, LLC; Notice of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-08

    ... From the Federal Register Online via the Government Printing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Terra-Gen Dixie Valley, LLC; TGP Dixie Development Company, LLC; New York Canyon, LLC; Notice of Filing December 30, 2009. Take notice that on December 24, 2009, Terra-Gen Dixie Valley, LLC, TGP Dixie Development...

  11. Tools for Designing, Evaluating, and Certifying NextGen Technologies and Procedures: Automation Roles and Responsibilities

    NASA Technical Reports Server (NTRS)

    Kanki, Barbara G.

    2011-01-01

    Barbara Kanki from NASA Ames Research Center will discuss research that focuses on the collaborations between pilots, air traffic controllers and dispatchers that will change in NextGen systems as automation increases and roles and responsibilities change. The approach taken by this NASA Ames team is to build a collaborative systems assessment template (CSAT) based on detailed task descriptions within each system to establish a baseline of the current operations. The collaborative content and context are delineated through the review of regulatory and advisory materials, policies, procedures and documented practices as augmented by field observations and interviews. The CSAT is developed to aid the assessment of key human factors and performance tradeoffs that result from considering different collaborative arrangements under NextGen system changes. In theory, the CSAT product may be applied to any NextGen application (such as Trajectory Based Operations) with specified ground and aircraft capabilities.

  12. Critical Issues on Materials for Gen-IV Reactors

    SciTech Connect

    Caro, M; Marian, J; Martinez, E; Erhart, P

    2009-02-27

    Within the LDRD on 'Critical Issues on Materials for Gen-IV Reactors' basic thermodynamics of the Fe-Cr alloy and accurate atomistic modeling were used to help develop the capability to predict hardening, swelling and embrittlement using the paradigm of Multiscale Materials Modeling. Approaches at atomistic and mesoscale levels were linked to build-up the first steps in an integrated modeling platform that seeks to relate in a near-term effort dislocation dynamics to polycrystal plasticity. The requirements originated in the reactor systems under consideration today for future sources of nuclear energy. These requirements are beyond the present day performance of nuclear materials and calls for the development of new, high temperature, radiation resistant materials. Fe-Cr alloys with 9-12% Cr content are the base matrix of advanced ferritic/martensitic (FM) steels envisaged as fuel cladding and structural components of Gen-IV reactors. Predictive tools are needed to calculate structural and mechanical properties of these steels. This project represents a contribution in that direction. The synergy between the continuous progress of parallel computing and the spectacular advances in the theoretical framework that describes materials have lead to a significant advance in our comprehension of materials properties and their mechanical behavior. We took this progress to our advantage and within this LDRD were able to provide a detailed physical understanding of iron-chromium alloys microstructural behavior. By combining ab-initio simulations, many-body interatomic potential development, and mesoscale dislocation dynamics we were able to describe their microstructure evolution. For the first time in the case of Fe-Cr alloys, atomistic and mesoscale were merged and the first steps taken towards incorporating ordering and precipitation effects into dislocation dynamics (DD) simulations. Molecular dynamics (MD) studies of the transport of self-interstitial, vacancy and point defect clusters in concentrated Fe-Cr alloys were performed for future diffusion data calculations. A recently developed parallel MC code with displacement allowed us to predict the evolution of the defect microstructures, local chemistry changes, grain boundary segregation and precipitation resulting from radiation enhanced diffusion. We showed that grain boundaries, dislocations and free surfaces are not preferential for alpha-prime precipitation, and explained experimental observations of short-range order (SRO) in Fe-rich FeCr alloys. Our atomistic studies of dislocation hardening allowed us to obtain dislocation mobility functions for BCC pure iron and Fe-Cr and determine for FCC metals the dislocation interaction with precipitates with a description to be used in Dislocation Dynamic (DD) codes. A Synchronous parallel Kinetic Monte Carlo code was developed and tested which promises to expand the range of applicability of kMC simulations. This LDRD furthered the limits of the available science on the thermodynamic and mechanic behavior of metallic alloys and extended the application of physically-based multiscale materials modeling to cases of severe temperature and neutron fluence conditions in advanced future nuclear reactors. The report is organized as follows: after a brief introduction, we present the research activities, and results obtained. We give recommendations on future LLNL activities that may contribute to the progress in this area, together with examples of possible research lines to be supported.

  13. NextGen Operations in a Simulated NY Area Airspace

    NASA Technical Reports Server (NTRS)

    Smith, Nancy M.; Parke, Bonny; Lee, Paul; Homola, Jeff; Brasil, Connie; Buckley, Nathan; Cabrall, Chris; Chevalley, Eric; Lin, Cindy; Morey, Susan; Omar, Faisal; Rein-Weston, Daphne; Yoo, Hyo-Sang

    2013-01-01

    A human-in-the-loop simulation conducted in the Airspace Operations Laboratory (AOL) at NASA Ames Research Center explored the feasibility of a Next Generation Air Transportation System (NextGen) solution to address airspace and airport capacity limitations in and around the New York metropolitan area. A week-long study explored the feasibility of a new Optimal Profile Descent (OPD) arrival into the airspace as well as a novel application of a Terminal Area Precision Scheduling and Spacing (TAPSS) enhancement to the Traffic Management Advisor (TMA) arrival scheduling tool to coordinate high volume arrival traffic to intersecting runways. In the simulation, four en route sector controllers and four terminal radar approach control (TRACON) controllers managed traffic inbound to Newark International Airport's primary runway, 22L, and its intersecting overflow runway, 11. TAPSS was used to generate independent arrival schedules for each runway and a traffic management coordinator participant adjusted the arrival schedule for each runway 11 aircraft to follow one of the 22L aircraft. TAPSS also provided controller-managed spacing tools (slot markers with speed advisories and timelines) to assist the TRACON controllers in managing the arrivals that were descending on OPDs. Results showed that the tools significantly decreased the occurrence of runway violations (potential go-arounds) when compared with a Baseline condition with no tools. Further, the combined use of the tools with the new OPD produced a peak arrival rate of over 65 aircraft per hour using instrument flight rules (IFR), exceeding the current maximum arrival rate at Newark Liberty International Airport (EWR) of 52 per hour under visual flight rules (VFR). Although the participants rated the workload as relatively low and acceptable both with and without the tools, they rated the tools as reducing their workload further. Safety and coordination were rated by most participants as acceptable in both conditions, although the TRACON Runway Coordinator (TRC) rated neither as acceptable in the Baseline condition. Regarding the role of the TRC, the two TRACON controllers handling the 11 arrivals indicated that the TRC was very much needed in the Baseline condition without tools, but not needed in the condition with tools. This indicates that the tools were providing much of the sequencing and spacing information that the TRC had supplied in the Baseline condition.

  14. GenMin: An enhanced genetic algorithm for global optimization

    NASA Astrophysics Data System (ADS)

    Tsoulos, Ioannis G.; Lagaris, I. E.

    2008-06-01

    A new method that employs grammatical evolution and a stopping rule for finding the global minimum of a continuous multidimensional, multimodal function is considered. The genetic algorithm used is a hybrid genetic algorithm in conjunction with a local search procedure. We list results from numerical experiments with a series of test functions and we compare with other established global optimization methods. The accompanying software accepts objective functions coded either in Fortran 77 or in C++. Program summaryProgram title: GenMin Catalogue identifier: AEAR_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAR_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 35 810 No. of bytes in distributed program, including test data, etc.: 436 613 Distribution format: tar.gz Programming language: GNU-C++, GNU-C, GNU Fortran 77 Computer: The tool is designed to be portable in all systems running the GNU C++ compiler Operating system: The tool is designed to be portable in all systems running the GNU C++ compiler RAM: 200 KB Word size: 32 bits Classification: 4.9 Nature of problem: A multitude of problems in science and engineering are often reduced to minimizing a function of many variables. There are instances that a local optimum does not correspond to the desired physical solution and hence the search for a better solution is required. Local optimization techniques are frequently trapped in local minima. Global optimization is hence the appropriate tool. For example, solving a nonlinear system of equations via optimization, employing a least squares type of objective, one may encounter many local minima that do not correspond to solutions (i.e. they are far from zero). Solution method: Grammatical evolution and a stopping rule. Running time: Depending on the objective function. The test example given takes only a few seconds to run.

  15. Gen Y Recruitment: Understanding Graduate Intentions to Join an Organisation Using the Theory of Planned Behaviour

    ERIC Educational Resources Information Center

    Warmerdam, Amanda; Lewis, Ioni; Banks, Tamara

    2015-01-01

    Purpose: Using the Theory of Planned Behaviour (TPB) framework, the purpose of this paper is to explore whether the standard TPB constructs explained variance in Generation Y (Gen Y) individuals' intentions to join their ideal organisation. Design/methodology/approach: A mixed methods approach was used featuring qualitative and quantitative…

  16. A Possible Genome To Architecture Project (GenToA) [The Meta-Genome Project?

    E-print Network

    Sloman, Aaron

    concern about the Human Genome project, comparing it with buying a book written in a language nobodyA Possible Genome To Architecture Project (GenToA) [The Meta-Genome Project?] Installed: 2 Aug 2010 can a genome specify an information-processing architecture that grows itself guided by interaction

  17. FutureGen: Pathway to Near-Zero Emissions and Sustainable Energy

    SciTech Connect

    Zitney, S.E.; Sarkus, T.A

    2007-11-04

    This presentation will highlight the U.S. Department of Energy’s (DOE) FutureGen project ? a $1 billion government-industry partnership to design, build, and operate a near-zero emissions coal-fueled power plant. The lead organization for the FutureGen initiative is the National Energy Technology Laboratory (NETL), a multi-purpose laboratory operated by the U.S. DOE’s Office of Fossil Energy. NETL has a mission to conduct R&D from fundamental science to technology demonstration for resolving the environmental, supply, and reliability constraints of producing and using fossil energy resources. The commercial-scale FutureGen R&D facility is a pathway toward future fossil-energy power plants that will produce hydrogen and electricity while nearly eliminating emissions, including carbon dioxide. The 275-megawatt FutureGen plant will initiate operations around 2012 and employ advanced coal gasification technology integrated with combined cycle electricity generation, hydrogen production, and carbon capture and sequestration. Low carbon emissions would be achieved by integrating CO2 capture and sequestration operations with the power plant.

  18. Simulated Task Environment for HCI Analysis of NextGen Maricel Medina-Mora

    E-print Network

    -effective environment that can be used to perform studies to analyze human computer interaction behavior. Keywords NextGen. The implementation of a new communication protocol requires changes at multiple levels, and human-in-the- loop walkthroughs, part-task, whole-task and multi-agent simulation experiments. The results of these experiments

  19. Drainage fracture networks in elastic solids with internal fluid gen-Maya Kobchenko1

    E-print Network

    Galland, Olivier

    epl draft Drainage fracture networks in elastic solids with internal fluid gen- eration Maya layer to fracture. The gas produced is drained on short length scales by diffusion and on long length scales by flow in a fracture network, which has topological properties that are intermediate between

  20. GWAS in a box: statistical and visual analytics of structured associations via GenAMap.

    PubMed

    Xing, Eric P; Curtis, Ross E; Schoenherr, Georg; Lee, Seunghak; Yin, Junming; Puniyani, Kriti; Wu, Wei; Kinnaird, Peter

    2014-01-01

    With the continuous improvement in genotyping and molecular phenotyping technology and the decreasing typing cost, it is expected that in a few years, more and more clinical studies of complex diseases will recruit thousands of individuals for pan-omic genetic association analyses. Hence, there is a great need for algorithms and software tools that could scale up to the whole omic level, integrate different omic data, leverage rich structure information, and be easily accessible to non-technical users. We present GenAMap, an interactive analytics software platform that 1) automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression data, and clinical or other macroscopic traits, and 2) provides new visualization tools specifically designed to aid in the exploration of association mapping results. Algorithmically, GenAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association mapping, which leverages various structures in the omic data. We demonstrate the function of GenAMap via a case study of the Brem and Kruglyak yeast dataset, and then apply it on a comprehensive eQTL analysis of the NIH heterogeneous stock mice dataset and report some interesting findings. GenAMap is available from http://sailing.cs.cmu.edu/genamap. PMID:24905018

  1. Mol Gen Genet (1988)211:266-271 Springer-Verlag1988

    E-print Network

    Haughn, George

    1988-01-01

    Mol Gen Genet (1988)211:266-271 © Springer-Verlag1988 Transformation with a mutant, and that it may be useful as a select- able marker for plant transformation experiments. Key words: Ti plasmid of achieving this is through the genetic transformation of plants to herbicide resistance. The prerequisites

  2. Plant MetGenMAP: an integrative analysis system for plant systems biology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have developed a web-based system, Plant MetGenMAP, which can identify significantly altered biochemical pathways and highly affected biological processes, predict functional roles of pathway genes, and potential pathway-related regulatory motifs from transcript and metabolite profile datasets. P...

  3. 225USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Constraints on Germination and

    E-print Network

    225USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Constraints on Germination and Emergence, soil source, and microclimate on viability, germination, emergence, and seedling size of Emory oak increased germination up to 5-fold. Germination did not decline between 0 and 35 days of storage. Acorn size

  4. Working with Gen Y Teachers: Dealing with a Changing Teacher Workforce

    ERIC Educational Resources Information Center

    Williamson, Ronald; Meyer-Looze, Catherine

    2010-01-01

    A significant change is coming to American classrooms. As Baby Boomer teachers retire and are replaced by members of Generation Y (born between 1977 and 1995) there is growing evidence that they come from a far different set of experiences, experiences that will shape their lives and their careers (Coggins, 2008). Members of Gen Y share several…

  5. GEN1 promotes Holliday junction resolution by a coordinated nick and counter-nick mechanism.

    PubMed

    Chan, Ying Wai; West, Stephen

    2015-12-15

    Holliday junctions (HJs) that physically link sister chromatids or homologous chromosomes are formed as intermediates during DNA repair by homologous recombination. Persistent recombination intermediates are acted upon by structure-selective endonucleases that are required for proper chromosome segregation at mitosis. Here, we have purified full-length human GEN1 protein and show that it promotes Holliday junction resolution by a mechanism that is analogous to that exhibited by the prototypic HJ resolvase E. coli RuvC. We find that GEN1 cleaves HJs by a nick and counter-nick mechanism involving dual co-ordinated incisions that lead to the formation of ligatable nicked duplex products. As observed with RuvC, cleavage of the first strand is rate limiting, while second strand cleavage is rapid. In contrast to RuvC, however, GEN1 is largely monomeric in solution, but dimerizes on the HJ. Using HJs containing non-cleavable phosphorothioate-containing linkages in one strand, we show that the two incisions can be uncoupled and that the first nick occurs upon GEN1 dimerization at the junction. These results indicate that the mechanism of HJ resolution is largely conserved from bacteria to man, despite a lack of sequence homology between the resolvases. PMID:26578604

  6. GWAS in a Box: Statistical and Visual Analytics of Structured Associations via GenAMap

    E-print Network

    Xing, Eric P.

    GWAS in a Box: Statistical and Visual Analytics of Structured Associations via GenAMap Eric P. XingAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association mapping, which://sailing.cs.cmu.edu/genamap. Citation: Xing EP, Curtis RE, Schoenherr G, Lee S, Yin J, et al. (2014) GWAS in a Box: Statistical

  7. Overview of NASA's Next Generation Air Transportation System (NextGen) Research

    NASA Technical Reports Server (NTRS)

    Swenson, Harry N.

    2009-01-01

    This slide presentation is an overview of the research for the Next Generation Air Transportation System (NextGen). Included is a review of the current air transportation system and the challenges of air transportation research. Also included is a review of the current research highlights and significant accomplishments.

  8. ShieldGen: Automatic Data Patch Generation for Unknown Vulnerabilities with Informed Probing

    E-print Network

    Locasto, Michael E.

    ShieldGen: Automatic Data Patch Generation for Unknown Vulnerabilities with Informed Probing generating a data patch or a vulnerability signature for an unknown vulnerability, given a zero-day attack. In this paper, we aim to automate this process and enable fast, patch-level pro- tection generation

  9. 55USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Oak Research Needs1

    E-print Network

    55USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Oak Research Needs1 Enoch F. Bell2 If you," but perhaps you have not heard about the oak tree that "wood knot," slight pun intended. It would oaks and oak woodlands. I will divide my brief remarks into biological and social aspects. Biological

  10. 251USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Sunshine Canyon Mitigation Oaks--

    E-print Network

    251USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Sunshine Canyon Mitigation Oaks the Sunshine Canyon Landfill located on the north side of the San Fernando Valley, CA. The extension plans the foundation for the success of this project. Sunshine Canyon Landfill is a large sanitary waste facility

  11. OGIP Calibration Memo CAL/GEN/92-024 THE OGIP FORMAT FOR FILES CONTAINING FILTER &

    E-print Network

    Nishikawa, Ken-Ichi

    1 OGIP Calibration Memo CAL/GEN/92-024 THE OGIP FORMAT FOR FILES CONTAINING FILTER & WINDOW for the storage of the transmission of a filter or window in front of an instrument as a function of energy-024 (Filter/Window Transmission File Format) 2 Log of Significant Changes Release Sections Changed Brief Notes

  12. Xylochloris irregularis gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccoid green alga

    E-print Network

    green alga JIR I´ NEUSTUPA 1 *, MAREK ELIA´ S1 , PAVEL SKALOUD 1 , YVONNE NE MCOVA´ 1 AND LENKA irregularis gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccoid green alga. Phycologia 50: 57­66. DOI: 10.2216/08-64.1 The phylogenetic diversity of subaerial coccoid green algae remains

  13. Hylodesmus singaporensis gen. et sp. nov., a new autosporic subaerial green alga (Scenedesmaceae,

    E-print Network

    Hylodesmus singaporensis gen. et sp. nov., a new autosporic subaerial green alga (Scenedesmaceae characterization of an autosporic coccoid green alga isolated from decaying wood in a natural forest in Singapore. Depending on culture conditions, this alga formed globular to irregularly oval solitary cells

  14. Page 1 of 4 GenMAPP Gene Database for Staphylococcus aureus (strain MRSA252)

    E-print Network

    Dahlquist, Kam D.

    Page 1 of 4 GenMAPP Gene Database for Staphylococcus aureus (strain MRSA252) Sa for Staphylococcus aureus (strain MRSA252) that was built by the Loyola Marymount University (LMU) Bioinformatics Database. 4. Gene Database Specifications a. Gene ID Systems This Staphylococcus aureus Gene Database

  15. LASER AUTOGENOUS BRAZING A NEW METHOD FOR JOINING DISSIMILAR METALS Gen Satoh, Y. Lawrence Yao

    E-print Network

    Yao, Y. Lawrence

    of dissimilar metals is a critical process for the future development and evolution of medical devices whichLASER AUTOGENOUS BRAZING ­ A NEW METHOD FOR JOINING DISSIMILAR METALS Paper #602 Gen Satoh, Y the properties of implantable medical devices. Many joints between dissimilar metals, however, suffer from

  16. GEN1 promotes Holliday junction resolution by a coordinated nick and counter-nick mechanism

    PubMed Central

    Chan, Ying Wai; West, Stephen

    2015-01-01

    Holliday junctions (HJs) that physically link sister chromatids or homologous chromosomes are formed as intermediates during DNA repair by homologous recombination. Persistent recombination intermediates are acted upon by structure-selective endonucleases that are required for proper chromosome segregation at mitosis. Here, we have purified full-length human GEN1 protein and show that it promotes Holliday junction resolution by a mechanism that is analogous to that exhibited by the prototypic HJ resolvase E. coli RuvC. We find that GEN1 cleaves HJs by a nick and counter-nick mechanism involving dual co-ordinated incisions that lead to the formation of ligatable nicked duplex products. As observed with RuvC, cleavage of the first strand is rate limiting, while second strand cleavage is rapid. In contrast to RuvC, however, GEN1 is largely monomeric in solution, but dimerizes on the HJ. Using HJs containing non-cleavable phosphorothioate-containing linkages in one strand, we show that the two incisions can be uncoupled and that the first nick occurs upon GEN1 dimerization at the junction. These results indicate that the mechanism of HJ resolution is largely conserved from bacteria to man, despite a lack of sequence homology between the resolvases. PMID:26578604

  17. Cryptometrion aestuescens gen. sp. nov. (Cryphonectriaceae) pathogenic to Eucalyptus in Indonesia

    E-print Network

    Cryptometrion aestuescens gen. sp. nov. (Cryphonectriaceae) pathogenic to Eucalyptus in Indonesia M, Indonesia. C Corresponding author. Email: Marieka.Gryzenhout@fabi.up.ac.za Abstract. The recently described on Eucalyptus. A recent investigation of dying Eucalyptus grandis clonal hedges in northern Sumatra, Indonesia

  18. Builders Challenge High Performance Builder Spotlight - NextGen Home, Las Vegas, Nevada

    SciTech Connect

    2009-01-01

    Building America Builders Challenge fact sheet on the NextGen demo home built in Las Vegas. The home has a Home Energy Rating System (HERS) index score of 44 with R-40 spray foam attic insulation, R-40 insulated concrete walls, and a 4kW DC solar laminate

  19. Page 1 of 4 GenMAPP Gene Database for Arabidopsis thaliana

    E-print Network

    Dahlquist, Kam D.

    Page 1 of 4 GenMAPP Gene Database for Arabidopsis thaliana At-Std_External_2009610.gdb ReadMe Last Gene Database for each species. This ReadMe describes a Gene Database for Arabidopsis thaliana Specifications a. Gene ID Systems This Arabidopsis thaliana Gene Database is UniProt-centric in that the main

  20. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 49 Nesting Chronology Of The Marbled Murrelet

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 49 Nesting Chronology Of The Marbled Murrelet, and fledgling Marbled Murrelets (Brachyramphus marmoratus) for which the fledging date could be estimated September, a breeding period of 182 days. Detailed information on the breeding chronology of the Marbled

  1. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 313 Marbled Murrelet Populations of Washington--

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 313 Marbled Murrelet Populations of Washington Eldridge, Bellingham, Washington 98225 Abstract: Marbled Murrelets occur in Puget Sound marine habitats data indicate that Marbled Murrelet abundance in Puget Sound is now lower than earlier this century

  2. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 151 Abstract: Most Marbled Murrelets (Brachyramphus marmoratus)

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 151 Abstract: Most Marbled Murrelets problems for Marbled Murrelets in fragmented forests. The use of detection frequencies in the selection. British Columbia supports a significant portion of the North American population of Marbled Murrelets

  3. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 255 Abstract: Marbled Murrelets (Brachyramphus marmoratus) vary

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 255 Abstract: Marbled Murrelets (Brachyramphus of kleptoparasitism. Marbled Murrelets (Brachyramphus marmoratus) occupy a variety of foraging habitats and vary of other seabird species. Because marbled murrelets may be subject to kleptoparasitism in these mixed

  4. SQLUnitGen: Test Case Generation for SQL Injection Yonghee Shin, Laurie Williams, Tao Xie

    E-print Network

    Young, R. Michael

    SQLUnitGen: Test Case Generation for SQL Injection Detection Yonghee Shin, Laurie Williams, Tao Xie be classified as input manipulation, such as SQL injection, cross site scripting, and buffer overflows detection, and automatic testing. We propose an approach for SQL injection vulnerability detection

  5. POWER-GEN `96 international. Book V - D. Operating plants. Volume 13-15

    SciTech Connect

    1996-12-31

    This is the fifth book in a six book set for the Power-Gen 96 International Conference and Exhibition. This book contains Volumes 13 through 15. Topics covered by volumes 13 through 15 include: performance enhancement, and operations & management. Subtopics include: hydro and cogeneration, particulate control systems, turbines, boilers, power plant chemistry, and preventive and predictive maintenance.

  6. GWAS in a Box: Statistical and Visual Analytics of Structured Associations via GenAMap

    PubMed Central

    Xing, Eric P.; Curtis, Ross E.; Schoenherr, Georg; Lee, Seunghak; Yin, Junming; Puniyani, Kriti; Wu, Wei; Kinnaird, Peter

    2014-01-01

    With the continuous improvement in genotyping and molecular phenotyping technology and the decreasing typing cost, it is expected that in a few years, more and more clinical studies of complex diseases will recruit thousands of individuals for pan-omic genetic association analyses. Hence, there is a great need for algorithms and software tools that could scale up to the whole omic level, integrate different omic data, leverage rich structure information, and be easily accessible to non-technical users. We present GenAMap, an interactive analytics software platform that 1) automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression data, and clinical or other macroscopic traits, and 2) provides new visualization tools specifically designed to aid in the exploration of association mapping results. Algorithmically, GenAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association mapping, which leverages various structures in the omic data. We demonstrate the function of GenAMap via a case study of the Brem and Kruglyak yeast dataset, and then apply it on a comprehensive eQTL analysis of the NIH heterogeneous stock mice dataset and report some interesting findings. GenAMap is available from http://sailing.cs.cmu.edu/genamap. PMID:24905018

  7. pGenN, a Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature

    PubMed Central

    Ding, Ruoyao; Arighi, Cecilia N.; Lee, Jung-Youn; Wu, Cathy H.; Vijay-Shanker, K.

    2015-01-01

    Background Automatically detecting gene/protein names in the literature and connecting them to databases records, also known as gene normalization, provides a means to structure the information buried in free-text literature. Gene normalization is critical for improving the coverage of annotation in the databases, and is an essential component of many text mining systems and database curation pipelines. Methods In this manuscript, we describe a gene normalization system specifically tailored for plant species, called pGenN (pivot-based Gene Normalization). The system consists of three steps: dictionary-based gene mention detection, species assignment, and intra species normalization. We have developed new heuristics to improve each of these phases. Results We evaluated the performance of pGenN on an in-house expertly annotated corpus consisting of 104 plant relevant abstracts. Our system achieved an F-value of 88.9% (Precision 90.9% and Recall 87.2%) on this corpus, outperforming state-of-art systems presented in BioCreative III. We have processed over 440,000 plant-related Medline abstracts using pGenN. The gene normalization results are stored in a local database for direct query from the pGenN web interface (proteininformationresource.org/pgenn/). The annotated literature corpus is also publicly available through the PIR text mining portal (proteininformationresource.org/iprolink/). PMID:26258475

  8. Merging and Spacing of Heterogeneous Aircraft in Support of NextGen

    E-print Network

    Egerstedt, Magnus

    Merging and Spacing of Heterogeneous Aircraft in Support of NextGen Rahul Chipalkatty1 , Philip Twu of aircraft. This paper provides a distributed merging and spacing algorithm that maximizes the throughput to reach an agreement on optimal merging times, with respect to a pairwise cost, while ensuring proper

  9. 76 FR 15039 - RTCA Government/Industry NextGen Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-18

    ... From the Federal Register Online via the Government Printing Office DEPARTMENT OF TRANSPORTATION Federal Aviation Administration RTCA Government/Industry NextGen Advisory Committee AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: Notice of RTCA Charter Renewal. SUMMARY: The FAA is...

  10. GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework.

    PubMed

    Parks, Donovan H; Mankowski, Timothy; Zangooei, Somayyeh; Porter, Michael S; Armanini, David G; Baird, Donald J; Langille, Morgan G I; Beiko, Robert G

    2013-01-01

    GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis. PMID:23922841

  11. GenGIS 2: Geospatial Analysis of Traditional and Genetic Biodiversity, with New Gradient Algorithms and an Extensible Plugin Framework

    PubMed Central

    Parks, Donovan H.; Mankowski, Timothy; Zangooei, Somayyeh; Porter, Michael S.; Armanini, David G.; Baird, Donald J.; Langille, Morgan G. I.; Beiko, Robert G.

    2013-01-01

    GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis. PMID:23922841

  12. Generation and selection of novel estrogen receptor ligands using the de novo structure-based design tool, SkelGen.

    PubMed

    Firth-Clark, Stuart; Willems, Henriëtte M G; Williams, Anthony; Harris, William

    2006-01-01

    A de novo design approach to generating novel estrogen receptor (ER) ligands is described. The SkelGen program was used to generate ligands in the active sites of seven crystal structures of ERalpha. Seventeen high-scoring, diverse structures were selected from the SkelGen output and synthesized without introducing any modifications to the structures. Five ligands, four of which are novel, showed < or = 25 microM affinity, with the best compound displaying an IC50 of 340 nM. SkelGen can, therefore, be a powerful tool for designing active molecules. PMID:16562994

  13. Mercury: Next-gen Data Analysis and Annotation Pipeline (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    SciTech Connect

    Sexton, David

    2012-06-01

    David Sexton (Baylor) gives a talk titled "Mercury: Next-gen Data Analysis and Annotation Pipeline" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  14. Mercury: Next-gen Data Analysis and Annotation Pipeline (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Sexton, David [Baylor

    2013-01-25

    David Sexton (Baylor) gives a talk titled "Mercury: Next-gen Data Analysis and Annotation Pipeline" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  15. 77 FR 52352 - Notice of Intent To Prepare an Environmental Impact Statement for the Rio Mesa Gen-Tie Project...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-29

    ...Mesa Gen-Tie Project and Possible Land Use Plan Amendment, Riverside County...resources, special management areas, land use, noise, paleontological resources...on the findings in the EIS. If a land use plan amendment is necessary,...

  16. Fottea 10(1): 7582, 2010 75 Phylogenetic position of Ooplanctella planoconvexa, gen. et comb. nova and

    E-print Network

    Fottea 10(1): 75­82, 2010 75 Phylogenetic position of Ooplanctella planoconvexa, gen. et comb. nova. nova, is proposed. Key words: 18S rDNA, Coenochloris, Echinocoleum, molecular phylogeny, Oocystaceae

  17. 78 FR 56263 - HydroGen Corp., QueryObject Systems Corp., Security Intelligence Technologies, Inc., Skins, Inc...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-12

    ... From the Federal Register Online via the Government Publishing Office SECURITIES AND EXCHANGE COMMISSION HydroGen Corp., QueryObject Systems Corp., Security Intelligence Technologies, Inc., Skins, Inc... and accurate information concerning the securities of Security Intelligence Technologies, Inc....

  18. Identification and Characterization of Key Human Performance Issues and Research in the Next Generation Air Transportation System (NextGen)

    NASA Technical Reports Server (NTRS)

    Lee, Paul U.; Sheridan, Tom; Poage, james L.; Martin, Lynne Hazel; Jobe, Kimberly K.

    2010-01-01

    This report identifies key human-performance-related issues associated with Next Generation Air Transportation System (NextGen) research in the NASA NextGen-Airspace Project. Four Research Focus Areas (RFAs) in the NextGen-Airspace Project - namely Separation Assurance (SA), Airspace Super Density Operations (ASDO), Traffic Flow Management (TFM), and Dynamic Airspace Configuration (DAC) - were examined closely. In the course of the research, it was determined that the identified human performance issues needed to be analyzed in the context of NextGen operations rather than through basic human factors research. The main gaps in human factors research in NextGen were found in the need for accurate identification of key human-systems related issues within the context of specific NextGen concepts and better design of the operational requirements for those concepts. By focusing on human-system related issues for individual concepts, key human performance issues for the four RFAs were identified and described in this report. In addition, mixed equipage airspace with components of two RFAs were characterized to illustrate potential human performance issues that arise from the integration of multiple concepts.

  19. Towards Structuring Unstructured GenBank Metadata for Enhancing Comparative Biological Studies

    PubMed Central

    Chen, Elizabeth S.; Sarkar, Indra Neil

    2011-01-01

    Within large sequence repositories such as GenBank there is a wealth of metadata providing contextual information that may enhance search and retrieval of relevant sequences for a range of subsequent analyses. One challenge is the use of free-text in these metadata fields where approaches are needed to extract, structure, and encode essential information. The goal of the present study was to explore the feasibility of using a combination of existing resources for annotating unstructured GenBank metadata, initially focusing on the “host” and “isolation_source” fields. This paper summarizes early results for 10 host organisms that include a characterization of associated isolation sources with respect to biomedical ontologies and semantic types. The findings from this preliminary study provide insights to the rich amount of information captured within these unstructured metadata, guidance for addressing the challenges and issues encountered, and highlight the potential value for enriching comparative biological studies towards improving human health. PMID:22211174

  20. Parametric Modeling of the Safety Effects of NextGen Terminal Maneuvering Area Conflict Scenarios

    NASA Technical Reports Server (NTRS)

    Rogers, William H.; Waldron, Timothy P.; Stroiney, Steven R.

    2011-01-01

    The goal of this work was to analytically identify and quantify the issues, challenges, technical hurdles, and pilot-vehicle interface issues associated with conflict detection and resolution (CD&R)in emerging operational concepts for a NextGen terminal aneuvering area, including surface operations. To this end, the work entailed analytical and trade studies focused on modeling the achievable safety benefits of different CD&R strategies and concepts in the current and future airport environment. In addition, crew-vehicle interface and pilot performance enhancements and potential issues were analyzed based on review of envisioned NextGen operations, expected equipage advances, and human factors expertise. The results of perturbation analysis, which quantify the high-level performance impact of changes to key parameters such as median response time and surveillance position error, show that the analytical model developed could be useful in making technology investment decisions.

  1. Neutron Arm Study and Calibration for the GEn Experiment at Thomas Jefferson National Laboratory

    SciTech Connect

    Timothy Ngo

    2007-07-01

    The measurement of the neutron electric form factor, GEn, will allow us to solve indirectly for the quark charge distribution inside of the neutron. With the equipment at Jefferson Lab we have measured GEn at four momentum transfer values of Q**2 at 1.3, 2.4 and 3.4 (GeV/c)**2 using a polarized electron beam and polarized Helium target. The scattered electrons off of the Helium target are detected in the BigBite spectrometer and the recoiling neutrons from the Helium are detected in the Neutron Arm, which is composed of an array of scintillators. The main focus of this thesis will be devoted to the geometry, timing and energy calibrations of the Neutron Arm.

  2. trome, trEST and trGEN: databases of predicted protein sequences

    PubMed Central

    Sperisen, Peter; Iseli, Christian; Pagni, Marco; Stevenson, Brian J.; Bucher, Philipp; Jongeneel, C. Victor

    2004-01-01

    We previously introduced two new protein databases (trEST and trGEN) of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Here, we present the updates made on these two databases plus a new database (trome), which uses alignments of EST data to HTG or full genomes to generate virtual transcripts and coding sequences. This new database is of higher quality and since it contains the information in a much denser format it is of much smaller size. These new databases are in a Swiss-Prot-like format and are updated on a weekly basis (trEST and trGEN) or every 3 months (trome). They can be downloaded by anonymous ftp from ftp://ftp.isrec.isb-sib.ch/pub/databases. PMID:14681469

  3. Gen 2.0 Mixer/Ejector Nozzle Test at LSAF June 1995 to July 1996

    NASA Technical Reports Server (NTRS)

    Arney, L. D.; Sandquist, D. L.; Forsyth, D. W.; Lidstone, G. L.; Long-Davis, Mary Jo (Technical Monitor)

    2005-01-01

    Testing of the HSCT Generation 2.0 nozzle model hardware was conducted at the Boeing Low Speed Aeroacoustic Facility, LSAF. Concurrent measurements of noise and thrust were made at critical takeoff design conditions for a variety of mixer/ejector model hardware. Design variables such as suppressor area ratio, mixer area ratio, liner type and thickness, ejector length, lobe penetration, and mixer chute shape were tested. Parallel testing was conducted at G.E.'s Cell 41 acoustic free jet facility to augment the LSAF test. The results from the Gen 2.0 testing are being used to help shape the current nozzle baseline configuration and guide the efforts in the upcoming Generation 2.5 and 3.0 nozzle tests. The Gen 2.0 results have been included in the total airplane system studies conducted at MDC and Boeing to provide updated noise and thrust performance estimates.

  4. Development of an Enhanced GenVARR™ (Generator Volt Ampere Reactive Reserve) System

    SciTech Connect

    Schatz, Joe E.

    2009-03-12

    Transmission system operators require near real time knowledge of reactive power capability to reliably operate large electric power transmission systems. Reactive power produced by, or capable of being produced by, a power generator is often estimated based on a series of mega volt amperes (MVA) capability curves for the generator. These curves indicate the ability of the generator to produce real and reactive power under a variety of conditions. In transmission planning and operating studies, it is often assumed, based on estimates for these capability curves, that the generator can provide its rated MVA capability output when needed for system stability However, generators may not always operate at levels depicted by the maximum MVA capability curve due to present constraints. Transmission system operators utilizing the generators’ capability curves for operation decisions regarding transmission system stability or for planning horizons may overestimate the capability of the generators to supply reactive power when required. Southern Company has enhanced GenVARR(TM), the system of plant data query, retrieval, and analysis and calculates the actual – not estimated -- remaining reactive power output capability. The remaining reactive output is considered spinning reserve and is displayed graphically to transmission control center and generating plant operators to identify real time VAR limits. GenVARR is capable of aggregating generators from a defined region, or other user selectable combinations, to represent the available reserves that the operators are specifically interested in. GenVARR(TM) has been put into live production operation and is expected to significantly improve the overall visibility of the reactive reserve capability of the system. This new version of GenVARR(TM) significantly enhances the products structure and performance, and enables links to other key transmission system operation tools.

  5. Dual-track CCS stakeholder engagement: Lessons learned from FutureGen in Illinois

    USGS Publications Warehouse

    Hund, G.; Greenberg, S.E.

    2011-01-01

    FutureGen, as originally planned, was to be the world's first coal-fueled, near-zero emissions power plant with fully integrated, 90% carbon capture and storage (CCS). From conception through siting and design, it enjoyed strong support from multiple stakeholder groups, which benefited the overall project. Understanding the stakeholder engagement process for this project provides valuable insights into the design of stakeholder programs for future CCS projects. FutureGen is one of few projects worldwide that used open competition for siting both the power plant and storage reservoir. Most site proposals were coordinated by State governments. It was unique in this and other respects relative to the site selection method used on other DOE-supported projects. At the time of site selection, FutureGen was the largest proposed facility designed to combine an integrated gasification combined cycle (IGCC) coal-fueled power plant with a CCS system. Stakeholder engagement by states and the industry consortium responsible for siting, designing, building, and operating the facility took place simultaneously and on parallel tracks. On one track were states spearheading state-wide site assessments to identify candidate sites that they wanted to propose for consideration. On the other track was a public-private partnership between an industry consortium of thirteen coal companies and electric utilities that comprised the FutureGen Alliance (Alliance) and the U.S. Department of Energy (DOE). The partnership was based on a cooperative agreement signed by both parties, which assigned the lead for siting to the Alliance. This paper describes the stakeholder engagement strategies used on both of these tracks and provides examples from the engagement process using the Illinois semi-finalist sites. ?? 2011 Published by Elsevier Ltd.

  6. Generalized background error covariance matrix model (GEN_BE v2.0)

    NASA Astrophysics Data System (ADS)

    Descombes, G.; Auligné, T.; Vandenberghe, F.; Barker, D. M.; Barré, J.

    2015-03-01

    The specification of state background error statistics is a key component of data assimilation since it affects the impact observations will have on the analysis. In the variational data assimilation approach, applied in geophysical sciences, the dimensions of the background error covariance matrix (B) are usually too large to be explicitly determined and B needs to be modeled. Recent efforts to include new variables in the analysis such as cloud parameters and chemical species have required the development of the code to GENerate the Background Errors (GEN_BE) version 2.0 for the Weather Research and Forecasting (WRF) community model. GEN_BE allows for a simpler, flexible, robust, and community-oriented framework that gathers methods used by some meteorological operational centers and researchers. We present the advantages of this new design for the data assimilation community by performing benchmarks of different modeling of B and showing some of the new features in data assimilation test cases. As data assimilation for clouds remains a challenge, we present a multivariate approach that includes hydrometeors in the control variables and new correlated errors. In addition, the GEN_BE v2.0 code is employed to diagnose error parameter statistics for chemical species, which shows that it is a tool flexible enough to implement new control variables. While the generation of the background errors statistics code was first developed for atmospheric research, the new version (GEN_BE v2.0) can be easily applied to other domains of science and chosen to diagnose and model B. Initially developed for variational data assimilation, the model of the B matrix may be useful for variational ensemble hybrid methods as well.

  7. MicroGen: a MIAME compliant web system for microarray experiment information and workflow management

    PubMed Central

    Burgarella, Sarah; Cattaneo, Dario; Pinciroli, Francesco; Masseroli, Marco

    2005-01-01

    Background Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Although they are routinely performed, spotted microarray experiments are complex procedures entailing several experimental steps and actors with different technical skills and roles. During an experiment, involved actors, who can also be located in a distance, need to access and share specific experiment information according to their roles. Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results. Results We developed MicroGen, a web system for managing information and workflow in the production pipeline of spotted microarray experiments. It is constituted of a core multi-database system able to store all data completely characterizing different spotted microarray experiments according to the Minimum Information About Microarray Experiments (MIAME) standard, and of an intuitive and user-friendly web interface able to support the collaborative work required among multidisciplinary actors and roles involved in spotted microarray experiment production. MicroGen supports six types of user roles: the researcher who designs and requests the experiment, the spotting operator, the hybridisation operator, the image processing operator, the system administrator, and the generic public user who can access the unrestricted part of the system to get information about MicroGen services. Conclusion MicroGen represents a MIAME compliant information system that enables managing workflow and supporting collaborative work in spotted microarray experiment production. PMID:16351755

  8. Complexity analysis of the Next Gen Air Traffic Management System: trajectory based operations.

    PubMed

    Lyons, Rhonda

    2012-01-01

    According to Federal Aviation Administration traffic predictions currently our Air Traffic Management (ATM) system is operating at 150 percent capacity; forecasting that within the next two decades, the traffic with increase to a staggering 250 percent [17]. This will require a major redesign of our system. Today's ATM system is complex. It is designed to safely, economically, and efficiently provide air traffic services through the cost-effective provision of facilities and seamless services in collaboration with multiple agents however, contrary the vision, the system is loosely integrated and is suffering tremendously from antiquated equipment and saturated airways. The new Next Generation (Next Gen) ATM system is designed to transform the current system into an agile, robust and responsive set of operations that are designed to safely manage the growing needs of the projected increasingly complex, diverse set of air transportation system users and massive projected worldwide traffic rates. This new revolutionary technology-centric system is dynamically complex and is much more sophisticated than it's soon to be predecessor. ATM system failures could yield large scale catastrophic consequences as it is a safety critical system. This work will attempt to describe complexity and the complex nature of the NextGen ATM system and Trajectory Based Operational. Complex human factors interactions within Next Gen will be analyzed using a proposed dual experimental approach designed to identify hazards, gaps and elicit emergent hazards that would not be visible if conducted in isolation. Suggestions will be made along with a proposal for future human factors research in the TBO safety critical Next Gen environment. PMID:22317416

  9. Stenolobulites n. gen., Early Permian ancestor of predominantly Late Permian Paragastrioceratid subfamily Pseudogastrioceratinae

    E-print Network

    Mikesh, D. L.; Glenister, B. F.; Furnish, W. M.

    1988-12-30

    in the earliest Permian Asselian Age, maintained high abundance and diversity throughout the remainder of that Period, and declined to extinction in the earliest Triassic Griesbachian Age. The subfamily Paragastrioceratinae, characterized by a ventral salient... PALEONTOLOGICAL CONTRIBUTIONS December 30, 1988 Paper 123 STENOLOBULITES N. GEN., EARLY PERMIAN ANCESTOR OF PREDOMINANTLY LATE PERMIAN PARAGASTRIOCERATID SUBFAMILY PSEUDOGASTRIOCERATINAE David L. Mikesh,' Brian F. Glenister, 2 and W. M. Furnish 2 '7993 South...

  10. Yamaguchia toyensis n. sp., n. gen. (Annelida, Clitellata, Lumbriculidae) from profundal lake habitat in Japan

    USGS Publications Warehouse

    Fend, S.V.; Ohtaka, A.

    2004-01-01

    Yamaguchia toyensis n. sp., n. gen. is described from an oligotrophic caldera lake, Lake Toya, Hokkaido, Japan. Although the taxonomic affinities are unknown, the genus differs from all other Lumbriculidae in having the combination of testes and atria in X, a single, prosoporous male funnel per atrium, and spermathecae in XI. Unlike other Japanese lakes that have thus far been surveyed, Lake Toya supports abundant populations of lumbriculids in the profundal benthos.

  11. GEN IV MATERIALS HANDBOOK BETA RELEASE FOR STRUCTURAL AND FUNCTIONAL EVALUATION

    SciTech Connect

    Ren, Weiju; Luttrell, Claire

    2006-09-12

    Development of the Gen IV Materials Handbook is briefly summarized up to date. Current status of the Handbook website construction is described. The developed Handbook components and access control of the beta version are discussed for the present evaluation release. Detailed instructions and examples are given to provide guidance for evaluators to browse the constructed parts and use all the currently developed functionalities of the Handbook in evaluation.

  12. Erection of a new genus Biura gen. nov., of the subtribe Aolina (Hemiptera: Cicadidae: Cicadinae: Dundubiini).

    PubMed

    Lee, Young June; Sanborn, Allen F

    2015-01-01

    A new genus, Biura gen. nov., is erected within the subtribe Aolina Boulard, 2012, designating Haphsa bicolora Sanborn, 2009 as the type species. This new genus is distinguished from all other genera in Aolina by the light-colored body lacking prominent markings, non-infuscated wings, very small and short male operculum, thin and long uncal lobes, and distinctly prominent basal lobes of the pygofer. PMID:26624729

  13. Geochemical Monitoring Considerations for the FutureGen 2.0 Project

    SciTech Connect

    Amonette, James E.; Johnson, Timothy A.; Spencer, Clayton F.; Zhong, Lirong; Szecsody, James E.; Vermeul, Vince R.

    2014-12-31

    Geochemical monitoring is an essential component of a suite of monitoring technologies designed to evaluate CO2 mass balance and detect possible loss of containment at the FutureGen 2.0 geologic sequestration site near Jacksonville, IL. This presentation gives an overview of the potential geochemical approaches and tracer technologies that were considered, and describes the evaluation process by which the most cost-effective and robust of these were selected for implementation

  14. Structures and stability of metal-doped GenM (n = 9, 10) clusters

    NASA Astrophysics Data System (ADS)

    Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua; Zhao, Li-Zhen; Zang, Qing-Jun; Wang, C. Z.; Ho, K. M.

    2015-06-01

    The lowest-energy structures of neutral and cationic GenM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge9 and Ge10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Gen clusters. However, the neutral and cationic FeGe9,10,MnGe9,10 and Ge10Al are cage-like with the metal atom encapsulated inside. Such cage-like transition metal doped Gen clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge9,10Fe and Ge9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.

  15. PanCoreGen - Profiling, detecting, annotating protein-coding genes in microbial genomes.

    PubMed

    Paul, Sandip; Bhardwaj, Archana; Bag, Sumit K; Sokurenko, Evgeni V; Chattopadhyay, Sujay

    2015-12-01

    A large amount of genomic data, especially from multiple isolates of a single species, has opened new vistas for microbial genomics analysis. Analyzing the pan-genome (i.e. the sum of genetic repertoire) of microbial species is crucial in understanding the dynamics of molecular evolution, where virulence evolution is of major interest. Here we present PanCoreGen - a standalone application for pan- and core-genomic profiling of microbial protein-coding genes. PanCoreGen overcomes key limitations of the existing pan-genomic analysis tools, and develops an integrated annotation-structure for a species-specific pan-genomic profile. It provides important new features for annotating draft genomes/contigs and detecting unidentified genes in annotated genomes. It also generates user-defined group-specific datasets within the pan-genome. Interestingly, analyzing an example-set of Salmonella genomes, we detect potential footprints of adaptive convergence of horizontally transferred genes in two human-restricted pathogenic serovars - Typhi and Paratyphi A. Overall, PanCoreGen represents a state-of-the-art tool for microbial phylogenomics and pathogenomics study. PMID:26456591

  16. CardioGenBase: A Literature Based Multi-Omics Database for Major Cardiovascular Diseases.

    PubMed

    V, Alexandar; Nayar, Pradeep G; Murugesan, R; Mary, Beaulah; P, Darshana; Ahmed, Shiek S S J

    2015-01-01

    Cardiovascular diseases (CVDs) account for high morbidity and mortality worldwide. Both, genetic and epigenetic factors are involved in the enumeration of various cardiovascular diseases. In recent years, a vast amount of multi-omics data are accumulated in the field of cardiovascular research, yet the understanding of key mechanistic aspects of CVDs remain uncovered. Hence, a comprehensive online resource tool is required to comprehend previous research findings and to draw novel methodology for understanding disease pathophysiology. Here, we have developed a literature-based database, CardioGenBase, collecting gene-disease association from Pubmed and MEDLINE. The database covers major cardiovascular diseases such as cerebrovascular disease, coronary artery disease (CAD), hypertensive heart disease, inflammatory heart disease, ischemic heart disease and rheumatic heart disease. It contains ~1,500 cardiovascular disease genes from ~2,4000 research articles. For each gene, literature evidence, ontology, pathways, single nucleotide polymorphism, protein-protein interaction network, normal gene expression, protein expressions in various body fluids and tissues are provided. In addition, tools like gene-disease association finder and gene expression finder are made available for the users with figures, tables, maps and venn diagram to fit their needs. To our knowledge, CardioGenBase is the only database to provide gene-disease association for above mentioned major cardiovascular diseases in a single portal. CardioGenBase is a vital online resource to support genome-wide analysis, genetic, epigenetic and pharmacological studies. PMID:26624015

  17. Taxonomy of the Proisotoma complex. V. Sexually dimorphic Ephemerotoma gen. nov. (Collembola: Isotomidae).

    PubMed

    Potapov, Mikhail; Kahrarian, Morteza; Deharveng, Louis; Shayanmehr, Masoumeh

    2015-01-01

    A new genus is proposed based on a new species from Iran, Ephemerotoma skarzynskii gen. et sp. nov., and three known species: E. huadongensis (Chen, 1985) comb. nov., E. multituberculata (Martynova, 1971) comb. nov. and E. porcella (Ellis, 1976) comb. nov. The genus shares the characters of Subisotoma Stach and Proctostephanus Börner and is distributed in southern areas of Eurasia (Eastern Mediterranean, Iran, Tajikistan, China). Ephemerotoma gen. nov. belongs to the Proisotoma-complex and is characterized by a simple maxillary palp, only 4 guards on labial papilla E and 2 prelabral chaetae. Four s-chaetae on Abd.V are arranged in two rows, two anterior and two posterior chaetae. All members of Ephemerotoma gen. nov. are redescribed or discussed based on type or fresh material, and a key to species of the genus is given. Scutisotoma potapovi Xie & Chen, 2008 is considered a synonym of E. huadongensis, while Proisotoma anopolitana is moved to the genus Proctostephanus. Sexual dimorphism is described for three species. PMID:26701434

  18. CardioGenBase: A Literature Based Multi-Omics Database for Major Cardiovascular Diseases

    PubMed Central

    V, Alexandar; Nayar, Pradeep G.; Murugesan, R.; Mary, Beaulah; P, Darshana; Ahmed, Shiek S. S. J.

    2015-01-01

    Cardiovascular diseases (CVDs) account for high morbidity and mortality worldwide. Both, genetic and epigenetic factors are involved in the enumeration of various cardiovascular diseases. In recent years, a vast amount of multi-omics data are accumulated in the field of cardiovascular research, yet the understanding of key mechanistic aspects of CVDs remain uncovered. Hence, a comprehensive online resource tool is required to comprehend previous research findings and to draw novel methodology for understanding disease pathophysiology. Here, we have developed a literature-based database, CardioGenBase, collecting gene-disease association from Pubmed and MEDLINE. The database covers major cardiovascular diseases such as cerebrovascular disease, coronary artery disease (CAD), hypertensive heart disease, inflammatory heart disease, ischemic heart disease and rheumatic heart disease. It contains ~1,500 cardiovascular disease genes from ~2,4000 research articles. For each gene, literature evidence, ontology, pathways, single nucleotide polymorphism, protein-protein interaction network, normal gene expression, protein expressions in various body fluids and tissues are provided. In addition, tools like gene-disease association finder and gene expression finder are made available for the users with figures, tables, maps and venn diagram to fit their needs. To our knowledge, CardioGenBase is the only database to provide gene-disease association for above mentioned major cardiovascular diseases in a single portal. CardioGenBase is a vital online resource to support genome-wide analysis, genetic, epigenetic and pharmacological studies. PMID:26624015

  19. Enhanced and Synthetic Vision for Terminal Maneuvering Area NextGen Operations

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Bailey, Randall E.; Ellis, Kyle K. E.; Norman, R. Michael; Williams, Steven P.; Arthur, Jarvis J., III; Shelton, Kevin J.; Prinzel, Lawrence J., III

    2011-01-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment with equivalent efficiency as visual operations. To meet this potential, research is needed for effective technology development and implementation of regulatory and design guidance to support introduction and use of SVS/EFVS advanced cockpit vision technologies in Next Generation Air Transportation System (NextGen) operations. A fixed-base pilot-in-the-loop simulation test was conducted at NASA Langley Research Center that evaluated the use of SVS/EFVS in NextGen low visibility ground (taxi) operations and approach/landing operations. Twelve crews flew approach and landing operations in a simulated NextGen Chicago O Hare environment. Various scenarios tested the potential for EFVS for operations in visibility as low as 1000 ft runway visibility range (RVR) and SVS to enable lower decision heights (DH) than can currently be flown today. Expanding the EFVS visual segment from DH to the runway in visibilities as low as 1000 RVR appears to be viable as touchdown performance was excellent without any workload penalties noted for the EFVS concept tested. A lower DH to 150 ft and/or possibly reduced visibility minima by virtue of SVS equipage appears to be viable when implemented on a Head-Up Display, but the landing data suggests further study for head-down implementations.

  20. Geophysical Monitoring Methods Evaluation for the FutureGen 2.0 Project

    DOE PAGESBeta

    Strickland, Chris E.; USA, Richland Washington; Vermeul, Vince R.; USA, Richland Washington; Bonneville, Alain; USA, Richland Washington; Sullivan, E. Charlotte; USA, Richland Washington; Johnson, Tim C.; USA, Richland Washington; et al

    2014-12-31

    A comprehensive monitoring program will be needed in order to assess the effectiveness of carbon sequestration at the FutureGen 2.0 carbon capture and storage (CCS) field-site. Geophysical monitoring methods are sensitive to subsurface changes that result from injection of CO2 and will be used for: (1) tracking the spatial extent of the free phase CO2 plume, (2) monitoring advancement of the pressure front, (3) identifying or mapping areas where induced seismicity occurs, and (4) identifying and mapping regions of increased risk for brine or CO2 leakage from the reservoir. Site-specific suitability and cost effectiveness were evaluated for a number ofmore »geophysical monitoring methods including: passive seismic monitoring, reflection seismic imaging, integrated surface deformation, time-lapse gravity, pulsed neutron capture logging, cross-borehole seismic, electrical resistivity tomography, magnetotellurics and controlled source electromagnetics. The results of this evaluation indicate that CO2 injection monitoring using reflection seismic methods would likely be difficult at the FutureGen 2.0 site. Electrical methods also exhibited low sensitivity to the expected CO2 saturation changes and would be affected by metallic infrastructure at the field site. Passive seismic, integrated surface deformation, time-lapse gravity, and pulsed neutron capture monitoring were selected for implementation as part of the FutureGen 2.0 storage site monitoring program.« less

  1. Geophysical Monitoring Methods Evaluation for the FutureGen 2.0 Project

    SciTech Connect

    Strickland, Chris E.; USA, Richland Washington; Vermeul, Vince R.; USA, Richland Washington; Bonneville, Alain; USA, Richland Washington; Sullivan, E. Charlotte; USA, Richland Washington; Johnson, Tim C.; USA, Richland Washington; Spane, Frank A.; USA, Richland Washington; Gilmore, Tyler J.; USA, Richland Washington

    2014-12-31

    A comprehensive monitoring program will be needed in order to assess the effectiveness of carbon sequestration at the FutureGen 2.0 carbon capture and storage (CCS) field-site. Geophysical monitoring methods are sensitive to subsurface changes that result from injection of CO2 and will be used for: (1) tracking the spatial extent of the free phase CO2 plume, (2) monitoring advancement of the pressure front, (3) identifying or mapping areas where induced seismicity occurs, and (4) identifying and mapping regions of increased risk for brine or CO2 leakage from the reservoir. Site-specific suitability and cost effectiveness were evaluated for a number of geophysical monitoring methods including: passive seismic monitoring, reflection seismic imaging, integrated surface deformation, time-lapse gravity, pulsed neutron capture logging, cross-borehole seismic, electrical resistivity tomography, magnetotellurics and controlled source electromagnetics. The results of this evaluation indicate that CO2 injection monitoring using reflection seismic methods would likely be difficult at the FutureGen 2.0 site. Electrical methods also exhibited low sensitivity to the expected CO2 saturation changes and would be affected by metallic infrastructure at the field site. Passive seismic, integrated surface deformation, time-lapse gravity, and pulsed neutron capture monitoring were selected for implementation as part of the FutureGen 2.0 storage site monitoring program.

  2. Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.

    PubMed Central

    Breider, Sven; Scheuner, Carmen; Schumann, Peter; Fiebig, Anne; Petersen, Jörn; Pradella, Silke; Klenk, Hans-Peter; Brinkhoff, Thorsten; Göker, Markus

    2014-01-01

    Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended. PMID:25157246

  3. FutureGen: Stepping-Stone to Sustainable Fossil-Fuel Power Generation

    SciTech Connect

    Zitney, S.E.

    2006-11-01

    This presentation will highlight the U.S. Department of Energy's FutureGen Initiative. The nearly $1 billion government-industry project is a stepping-stone toward future coal-fired power plants that will produce hydrogen and electricity with zero-emissions, including carbon dioxide. The 275-megawatt FutureGen plant will initiate operations around 2012 and employ advanced coal gasification technology integrated with combined cycle electricity generation, hydrogen production, and carbon capture and sequestration. The initiative is a response to a presidential directive to develop a hydrogen economy by drawing upon the best scientific research to address the issue of global climate change. The FutureGen plant will be based on cutting-edge power generation technology as well as advanced carbon capture and sequestration systems. The centerpiece of the project will be coal gasification technology that can eliminate common air pollutants such as sulfur dioxide and nitrogen oxides and convert them to useable by-products. Gasification will convert coal into a highly enriched hydrogen gas, which can be burned much more cleanly than directly burning the coal itself. Alternatively, the hydrogen can be used in a fuel cell to produce ultra-clean electricity, or fed to a refinery to help upgrade petroleum products. Carbon sequestration will also be a key feature that will set the Futuregen plant apart from other electric power plant projects. The initial goal will be to capture 90 percent of the plant's carbon dioxide, but capture of nearly 100 percent may be possible with advanced technologies. Once captured, the carbon dioxide will be injected as a compressed fluid deep underground, perhaps into saline reservoirs. It could even be injected into oil or gas reservoirs, or into unmineable coal seams, to enhance petroleum or coalbed methane recovery. The ultimate goal for the FutureGen plant is to show how new technology can eliminate environmental concerns over the future use of coal--the most abundant fossil fuel in the United States with supplies projected to last 250 years. FutureGen's co-production of power and hydrogen will also serve as a stepping-stone to an environmentally sustainable energy future.

  4. GEN1 from a thermophilic fungus is functionally closely similar to non-eukaryotic junction-resolving enzymes.

    PubMed

    Freeman, Alasdair D J; Liu, Yijin; Déclais, Anne-Cécile; Gartner, Anton; Lilley, David M J

    2014-12-12

    Processing of Holliday junctions is essential in recombination. We have identified the gene for the junction-resolving enzyme GEN1 from the thermophilic fungus Chaetomium thermophilum and expressed the N-terminal 487-amino-acid section. The protein is a nuclease that is highly selective for four-way DNA junctions, cleaving 1nt 3' to the point of strand exchange on two strands symmetrically disposed about a diagonal axis. CtGEN1 binds to DNA junctions as a discrete homodimer with nanomolar affinity. Analysis of the kinetics of cruciform cleavage shows that cleavage of the second strand occurs an order of magnitude faster than the first cleavage so as to generate a productive resolution event. All these properties are closely similar to those described for bacterial, phage and mitochondrial junction-resolving enzymes. CtGEN1 is also similar in properties to the human enzyme but lacks the problems with aggregation that currently prevent detailed analysis of the latter protein. CtGEN1 is thus an excellent enzyme with which to engage in biophysical and structural analysis of eukaryotic GEN1. PMID:25315822

  5. Data-link and surface map traffic intent displays for NextGen 4DT and equivalent visual surface operations

    NASA Astrophysics Data System (ADS)

    Shelton, Kevin J.; Prinzel, Lawrence (Lance) J., III; Arthur, Jarvis (Trey) J., III; Jones, Denise R.; Allamandola, Angela S.; Bailey, Randall E.

    2009-05-01

    By 2025, U.S. air traffic is predicted to increase 3-fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a consortium of industry, academia and government agencies have proposed a revolutionary new concept for U.S. aviation operations, termed the Next Generation Air Transportation System or "NextGen". Many key capabilities are being identified to enable NextGen, including the concept of "net-centric" operations whereby each aircraft and air services provider shares information to allow real-time adaptability to ever-changing factors such as weather, traffic, flight trajectories, and security. Data-link is likely to be the primary source of communication in NextGen. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen.

  6. GenDrux: A biomedical literature search system to identify gene expression-based drug sensitivity in breast cancer

    PubMed Central

    2011-01-01

    Background This paper describes the development of a web-based tool, GenDrux, which extracts and presents (over the Internet) information related to the disease-gene-drug nexus. This information is archived from the relevant biomedical literature using automated methods. GenDrux is designed to alleviate the difficulties of manually processing the vast biomedical literature to identify disease-gene-drug relationships. GenDrux will evolve with the literature without additional algorithmic modifications. Results GenDrux, a pilot system, is developed in the domain of breast cancer and can be accessed at http://www.microarray.uab.edu/drug_gene.pl. GenDrux can be queried based on drug, gene and/or disease name. From over 8,000 relevant abstracts from the biomedical literature related to breast cancer, we have archived a corpus of more than 4,000 articles that depict gene expression-drug activity relationships for breast cancer and related cancers. The archiving process has been automated. Conclusions The successful development, implementation, and evaluation of this and similar systems when created may provide clinicians with a tool for literature management, clinical decision making, thus setting the platform for personalized therapy in the future. PMID:21545721

  7. Data-Link and Surface Map Traffic Intent Displays for NextGen 4DT and Equivalent Visual Surface Operations

    NASA Technical Reports Server (NTRS)

    Shelton, Kevin J.; Prinzel, Lawrence J., III; Arthur, Jarvis J., III; Jones, Deise R.; Allamandola, Angela S.; Bailey, Randall E.

    2009-01-01

    By 2025, U.S. air traffic is predicted to increase 3-fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a consortium of industry, academia and government agencies have proposed a revolutionary new concept for U.S. aviation operations, termed the Next Generation Air Transportation System or "NextGen". Many key capabilities are being identified to enable NextGen, including the concept of "net-centric" operations whereby each aircraft and air services provider shares information to allow real-time adaptability to ever-changing factors such as weather, traffic, flight trajectories, and security. Data-link is likely to be the primary source of communication in NextGen. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen.

  8. GEN1 from a Thermophilic Fungus Is Functionally Closely Similar to Non-Eukaryotic Junction-Resolving Enzymes

    PubMed Central

    Freeman, Alasdair D.J.; Liu, Yijin; Déclais, Anne-Cécile; Gartner, Anton; Lilley, David M.J.

    2014-01-01

    Processing of Holliday junctions is essential in recombination. We have identified the gene for the junction-resolving enzyme GEN1 from the thermophilic fungus Chaetomium thermophilum and expressed the N-terminal 487-amino-acid section. The protein is a nuclease that is highly selective for four-way DNA junctions, cleaving 1 nt 3? to the point of strand exchange on two strands symmetrically disposed about a diagonal axis. CtGEN1 binds to DNA junctions as a discrete homodimer with nanomolar affinity. Analysis of the kinetics of cruciform cleavage shows that cleavage of the second strand occurs an order of magnitude faster than the first cleavage so as to generate a productive resolution event. All these properties are closely similar to those described for bacterial, phage and mitochondrial junction-resolving enzymes. CtGEN1 is also similar in properties to the human enzyme but lacks the problems with aggregation that currently prevent detailed analysis of the latter protein. CtGEN1 is thus an excellent enzyme with which to engage in biophysical and structural analysis of eukaryotic GEN1. PMID:25315822

  9. GenTegra DNA Tubes is another proprietary technology for stor-ing purified DNA in a `bone-dry', water-free environment. This new

    E-print Network

    Cai, Long

    GenTegra DNA Tubes is another proprietary technology for stor- ing purified DNA in a `bone source of DNA for genetic testing and population genetics, including methods such as short tandem repeat-region GenPlate for storing DNA, blood and bacterial clones at room temperature in the dry state. advertising

  10. Next Gen NEAR: Near Earth Asteroid Human Robotic Precursor Mission Concept

    NASA Technical Reports Server (NTRS)

    Rivkin, Andrew S.; Kirby, Karen; Cheng, Andrew F.; Gold, Robert; Kelly, Daniel; Reed, Cheryl; Abell, Paul; Garvin, James; Landis, Rob

    2012-01-01

    Asteroids have long held the attention of the planetary science community. In particular, asteroids that evolve into orbits near that of Earth, called near-Earth objects (NEO), are of high interest as potential targets for exploration due to the relative ease (in terms of delta V) to reach them. NASA's Flexible Path calls for missions and experiments to be conducted as intermediate steps towards the eventual goal of human exploration of Mars; piloted missions to NEOs are such example. A human NEO mission is a valuable exploratory step beyond the Earth-Moon system enhancing capabilities that surpass our current experience, while also developing infrastructure for future mars exploration capabilities. To prepare for a human rendezvous with an NEO, NASA is interested in pursuing a responsible program of robotic NEO precursor missions. Next Gen NEAR is such a mission, building on the NEAR Shoemaker mission experience at the JHU/APL Space Department, to provide an affordable, low risk solution with quick data return. Next Gen NEAR proposes to make measurements needed for human exploration to asteroids: to demonstrate proximity operations, to quantify hazards for human exploration and to characterize an environment at a near-Earth asteroid representative of those that may be future human destinations. The Johns Hopkins University Applied Physics Laboratory has demonstrated exploration-driven mission feasibility by developing a versatile spacecraft design concept using conventional technologies that satisfies a set of science, exploration and mission objectives defined by a concept development team in the summer of 2010. We will describe the mission concept and spacecraft architecture in detail. Configuration options were compared with the mission goals and objectives in order to select the spacecraft design concept that provides the lowest cost, lowest implementation risk, simplest operation and the most benefit for the mission implementation. The Next Gen NEAR spacecraft was designed to support rendezvous with a range of candidate asteroid targets and could easily be launched with one of several NASA launch vehicles. The Falcon 9 launch vehicle supports a Next Gen NEAR launch to target many near-Earth asteroids under consideration that could be reached with a C3 of 18 km2/sec2 or less, and the Atlas V-401 provides added capability supporting launch to NEAs that require more lift capacity while at the same time providing such excess lift capability that another payload of opportunity could be launch in conjunction with Next Gen NEAR. Next Gen NEAR will measure and interact with the target surface in ways never undertaken at an asteroid, and will prepare for first human precursor mission by demonstrating exploration science operations at an accessible NEO. This flexible mission and spacecraft design concept supports target selection based on upcoming Earth-based observations and also provides opportunities for co-manifest & international partnerships. JHU/APL has demonstrated low cost, low risk, high impact missions and this mission will help to prepare NASA for human NEO exploration by combining the best of NASA s human and robotic exploration capabilities.

  11. ‘LungGENS’: a web-based tool for mapping single-cell gene expression in the developing lung

    PubMed Central

    Du, Yina; Guo, Minzhe; Whitsett, Jeffrey A; Xu, Yan

    2015-01-01

    We developed LungGENS (Lung Gene Expression iN Single-cell), a web-based bioinformatics resource for querying single-cell gene expression databases by entering a gene symbol or a list of genes or selecting a cell type of their interest. Gene query provides quantitative RNA expression of the gene of interest in each lung cell type. Cell type query returns associated selective gene signatures and genes encoding cell surface markers and transcription factors in interactive heatmap and tables. LungGENS will be broadly applicable in respiratory research, providing a cell-specific RNA expression resource at single-cell resolution. LungGENS is freely available for non-commercial use at https://research.cchmc.org/pbge/lunggens/default.html. PMID:26130332

  12. Use of GenMAPP and MAPPFinder to analyse pathways involved in chickens infected with the protozoan parasite Eimeria

    PubMed Central

    Prickett, Dennis; Watson, Michael

    2009-01-01

    Background Microarrays allow genome-wide assays of gene expression. There is a need for user-friendly software to visualise and analyse these data. Analysing microarray data in the context of biological pathways is now common, and several tools exist. Results We describe the use of MAPPFinder, a component of GenMAPP to characterise the biological pathways affected in chickens infected with the protozoan parasite Eimeria. Several pathways were significantly affected based on the unadjusted p-value, including several immune-system pathways. Conclusion GenMAPP/MAPPFinder provides a means to rapidly visualise pathways affected in microarray studies. However, it relies on good genome annotation and having genes reliably linked to pathway objects. We show that GenMAPP/MAPPFinder can produce useful results, and as the annotation of the chicken genome improves, so will the level of information gained. PMID:19615120

  13. 'LungGENS': a web-based tool for mapping single-cell gene expression in the developing lung.

    PubMed

    Du, Yina; Guo, Minzhe; Whitsett, Jeffrey A; Xu, Yan

    2015-11-01

    We developed LungGENS (Lung Gene Expression iN Single-cell), a web-based bioinformatics resource for querying single-cell gene expression databases by entering a gene symbol or a list of genes or selecting a cell type of their interest. Gene query provides quantitative RNA expression of the gene of interest in each lung cell type. Cell type query returns associated selective gene signatures and genes encoding cell surface markers and transcription factors in interactive heatmap and tables. LungGENS will be broadly applicable in respiratory research, providing a cell-specific RNA expression resource at single-cell resolution. LungGENS is freely available for non-commercial use at https://research.cchmc.org/pbge/lunggens/default.html. PMID:26130332

  14. Enhanced Flight Vision Systems and Synthetic Vision Systems for NextGen Approach and Landing Operations

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Bailey, Randall E.; Ellis, Kyle K. E.; Williams, Steven P.; Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Shelton, Kevin J.

    2013-01-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment with equivalent efficiency as visual operations. To meet this potential, research is needed for effective technology development and implementation of regulatory standards and design guidance to support introduction and use of SVS/EFVS advanced cockpit vision technologies in Next Generation Air Transportation System (NextGen) operations. A fixed-base pilot-in-the-loop simulation test was conducted at NASA Langley Research Center that evaluated the use of SVS/EFVS in NextGen low visibility approach and landing operations. Twelve crews flew approach and landing operations in a simulated NextGen Chicago O'Hare environment. Various scenarios tested the potential for using EFVS to conduct approach, landing, and roll-out operations in visibility as low as 1000 feet runway visual range (RVR). Also, SVS was tested to evaluate the potential for lowering decision heights (DH) on certain instrument approach procedures below what can be flown today. Expanding the portion of the visual segment in which EFVS can be used in lieu of natural vision from 100 feet above the touchdown zone elevation to touchdown and rollout in visibilities as low as 1000 feet RVR appears to be viable as touchdown performance was acceptable without any apparent workload penalties. A lower DH of 150 feet and/or possibly reduced visibility minima using SVS appears to be viable when implemented on a Head-Up Display, but the landing data suggests further study for head-down implementations.

  15. Evaluation of Gen-Probe's Histoplasma capsulatum and Cryptococcus neoformans AccuProbes.

    PubMed Central

    Huffnagle, K E; Gander, R M

    1993-01-01

    Gen-Probe's DNA probes were evaluated for use in the identification of clinical isolates of Histoplasma capsulatum var. capsulatum and Cryptococcus neoformans. Ninety-five mould-phase fungi were probed, including 41 isolates of H. capsulatum var. capsulatum. Similarly, 98 yeasts, including 42 C. neoformans isolates, were examined by using the C. neoformans DNA probe. In the study, both probes demonstrated 100% specificity and 100% sensitivity. Their use in the clinical laboratory may significantly reduce the time required for definitive identification of fungi. PMID:8432829

  16. Modeling Off-Nominal Recovery in NextGen Terminal-Area Operations

    NASA Technical Reports Server (NTRS)

    Callantine, Todd J.

    2011-01-01

    Robust schedule-based arrival management requires efficient recovery from off-nominal situations. This paper presents research on modeling off-nominal situations and plans for recovering from them using TRAC, a route/airspace design, fast-time simulation, and analysis tool for studying NextGen trajectory-based operations. The paper provides an overview of a schedule-based arrival-management concept and supporting controller tools, then describes TRAC implementations of methods for constructing off-nominal scenarios, generating trajectory options to meet scheduling constraints, and automatically producing recovery plans.

  17. Irradiation effects in oxide dispersion strengthened (ODS) Ni-base alloys for Gen. IV nuclear reactors

    NASA Astrophysics Data System (ADS)

    Oono, Naoko; Ukai, Shigeharu; Kondo, Sosuke; Hashitomi, Okinobu; Kimura, Akihiko

    2015-10-01

    Oxide particle dispersion strengthened (ODS) Ni-base alloys are irradiated by using simulation technique (Fe/He dual-ion irradiation) to investigate the reliability to Gen. IV high-temperature reactors. The fine oxide particles with less than 10 nm in average size and approximately 8.0 × 1022 m-3 in number density remained after 101 dpa irradiation. The tiny helium bubbles were inside grains, not at grain-boundaries; it is advantageous effect of oxide particles which trap the helium atoms at the particle-matrix interface. Ni-base ODS alloys demonstrated their great ability to overcome He embrittlement.

  18. Tapajos cristinae gen. n., sp. n. (Diptera: Chironomidae: Chironominae) from the Neotropical region.

    PubMed

    Trivinho-Strixino, Susana; da Silva, Fabio Laurindo; de Oliveira, Caroline Silva Neubern

    2013-01-01

    A new genus of non-biting midges, Tapajos gen. n., is erected for T cristinae sp. n. from the Neotropical region, and placed in the subfamily Chironominae, tribe Chironomini. Adult males are characterized by the combination of bare eyes; antenna with 11 flagellomeres; antepronotal lobes fused medially; fore tibia with inner scale broad and rounded; superior volsella with a long sickle shaped, bare part arising from the distal lateral corner of a globose, densely trichiose base; inferior volsella sub-cylindrical, surpassing the anal point, distally setose and slightly expanded. PMID:26106701

  19. Bias explorer: measurements of compositional bias in EMBL and GenBank sequence files.

    PubMed

    Fuglsang, Anders

    2004-11-01

    A Windows application for compositional analysis of sequenced genomes (EMBL or GenBank flat files) is available as freeware. The application allows the user to quantify word bias using Markov chain analysis and it allows the user to generate sliding window data for GC-skew, AT-skew, purine excess, keto excess and discrete word counts. The mathematical routines reside in a dynamic link library (DLL), which can be used independently by other applications. The software is available for download at http://www.dfuni.dk/~anfu/Bioinformatics/Main.htm. PMID:15702383

  20. Gen IV Materials Handbook Functionalities and Operation (4A) Handbook Version 4.0

    SciTech Connect

    Ren, Weiju

    2013-09-01

    This document is prepared for navigation and operation of the Gen IV Materials Handbook, with architecture description and new user access initiation instructions. Development rationale and history of the Handbook is summarized. The major development aspects, architecture, and design principles of the Handbook are briefly introduced to provide an overview of its past evolution and future prospects. Detailed instructions are given with examples for navigating the constructed Handbook components and using the main functionalities. Procedures are provided in a step-by-step fashion for Data Upload Managers to upload reports and data files, as well as for new users to initiate Handbook access.

  1. Foveocrotaphus gen. n. and F. burmanicus sp. n.: a new genus and species of Physocrotaphini from Myanmar (Coleoptera: Carabidae: Anthiinae).

    PubMed

    Anichtchenko, Alexander

    2014-01-01

    Foveocrotaphus gen. nov. and new species F. burmanicus from Myanmar is described. The new genus is similar to Physocrotaphus Parry, with respect to shape and structure of ligula and paraglossae. The two genera can be diagnosed easily by median tooth of mentum, bifid in Physocrotaphus, i.e. Foveocrotaphus gen. n. has simple, narrow and pointed. Is distinguishable from all other known Physocrotaphini genera by narrower pronotum, very stout ligula combined with long and simple median tooth of mentum and by male sternites 2 and 3 with one big shared median depression. PMID:24869526

  2. Paragnomoxyala gen. nov. (Xyalidae, Monhysterida, Nematoda) from the East China Sea.

    PubMed

    Jiang, Weijun; Huang, Yong

    2015-01-01

    A new genus, Paragnomoxyala gen. nov., and a new species, Paragnomoxyala breviseta sp. nov. are described from the East China Sea. Paragnomoxyala gen. nov. is characterized by having large funnel-shaped buccal cavity with cuticularized walls and extended anteriorly; lips very high; striated cuticle; four cephalic setae, absence of outer labial setae; circular amphidial fovea; straight spicules and absence of gubernaculum; tail conico-cylindrical with three terminal setae; female monodelphic with an anterior outstretched ovary. It differs from similar genera by having a large buccal cavity unique in Xyalidae, straight spicules, lacking gubernaculum, and conico-cylindrical tail with terminal setae. Paragnomoxyala breviseta sp. nov. is characterized by having a large funnel-shaped buccal cavity, with cuticularized walls and extended anteriorly, 1.6-1.8 hd long and 63-79% cbd wide; four cephalic setae 3-4 µm long; circular amphids 6-9 µm in diameter; spicules straight but slightly bent at both ends; absence of gubernaculum and precloacal supplement. PMID:26624631

  3. Flight Deck Technologies to Enable NextGen Low Visibility Surface Operations

    NASA Technical Reports Server (NTRS)

    Prinzel, Lawrence (Lance) J., III; Arthur, Jarvis (Trey) J.; Kramer, Lynda J.; Norman, Robert M.; Bailey, Randall E.; Jones, Denise R.; Karwac, Jerry R., Jr.; Shelton, Kevin J.; Ellis, Kyle K. E.

    2013-01-01

    Many key capabilities are being identified to enable Next Generation Air Transportation System (NextGen), including the concept of Equivalent Visual Operations (EVO) . replicating the capacity and safety of today.s visual flight rules (VFR) in all-weather conditions. NASA is striving to develop the technologies and knowledge to enable EVO and to extend EVO towards a Better-Than-Visual operational concept. This operational concept envisions an .equivalent visual. paradigm where an electronic means provides sufficient visual references of the external world and other required flight references on flight deck displays that enable Visual Flight Rules (VFR)-like operational tempos while maintaining and improving safety of VFR while using VFR-like procedures in all-weather conditions. The Langley Research Center (LaRC) has recently completed preliminary research on flight deck technologies for low visibility surface operations. The work assessed the potential of enhanced vision and airport moving map displays to achieve equivalent levels of safety and performance to existing low visibility operational requirements. The work has the potential to better enable NextGen by perhaps providing an operational credit for conducting safe low visibility surface operations by use of the flight deck technologies.

  4. †Kenyaichthyidae fam. nov. and †Kenyaichthys gen. nov. – First Record of a Fossil Aplocheiloid Killifish (Teleostei, Cyprinodontiformes)

    PubMed Central

    Altner, Melanie; Reichenbacher, Bettina

    2015-01-01

    The extant Cyprinodontiformes (killifishes) with their two suborders Cyprinodontoidei and Aplocheiloidei represent a diverse and well-studied group of fishes. However, their fossil record is comparatively sparse and has so far yielded members of the Cyprinodontoidei only. Here we report on cyprinodontiform fossils from the upper Miocene Lukeino Formation in the Tugen Hills of the Central Rift Valley of Kenya, which represent the first fossil record of an aplocheiloid killifish. A total of 169 specimens - mostly extraordinarily well preserved - and a sample of ten extant cyprinodontiform species were studied on the basis of morphometrics, meristics and osteology. A phylogenetic analysis using PAUP was also conducted for the fossils. Both the osteological data and the phylogenetic analysis provide strong evidence for the assignment of the fossils to the Aplocheiloidei, and justify the definition of the new family †Kenyaichthyidae, the new genus †Kenyaichthys and the new species †K. kipkechi sp. nov. The phylogenetic analysis unexpectedly places †Kenyaichthys gen. nov. in a sister relationship to the Rivulidae (a purely Neotropical group), a probable explanation might be lack of available synapomorphies for the Rivulidae, Nothobranchiidae and Aplocheilidae. The specimens of †K. kipkechi sp. nov. show several polymorphic characters and large overlap in meristic traits, which justifies their interpretation as a species flock in statu nascendi. Patterns of variation in neural and haemal spine dimensions in the caudal vertebrae of †Kenyaichthys gen. nov. and the extant species studied indicate that some previously suggested synapomorphies of the Cyprinodontoidei and Aplocheiloidei need to be revised. PMID:25923654

  5. Structural materials for Gen-IV nuclear reactors: Challenges and opportunities

    NASA Astrophysics Data System (ADS)

    Murty, K. L.; Charit, I.

    2008-12-01

    Generation-IV reactor design concepts envisioned thus far cater toward a common goal of providing safer, longer lasting, proliferation-resistant and economically viable nuclear power plants. The foremost consideration in the successful development and deployment of Gen-IV reactor systems is the performance and reliability issues involving structural materials for both in-core and out-of-core applications. The structural materials need to endure much higher temperatures, higher neutron doses and extremely corrosive environment, which are beyond the experience of the current nuclear power plants. Materials under active consideration for use in different reactor components include various ferritic/martensitic steels, austenitic stainless steels, nickel-base superalloys, ceramics, composites, etc. This paper presents a summary of various Gen-IV reactor concepts, with emphasis on the structural materials issues depending on the specific application areas. This paper also discusses the challenges involved in using the existing materials under both service and off-normal conditions. Tasks become increasingly complex due to the operation of various fundamental phenomena like radiation-induced segregation, radiation-enhanced diffusion, precipitation, interactions between impurity elements and radiation-produced defects, swelling, helium generation and so forth. Further, high temperature capability (e.g. creep properties) of these materials is a critical, performance-limiting factor. It is demonstrated that novel alloy and microstructural design approaches coupled with new materials processing and fabrication techniques may mitigate the challenges, and the optimum system performance may be achieved under much demanding conditions.

  6. The Plant Genome Integrative Explorer Resource: PlantGenIE.org.

    PubMed

    Sundell, David; Mannapperuma, Chanaka; Netotea, Sergiu; Delhomme, Nicolas; Lin, Yao-Cheng; Sjödin, Andreas; Van de Peer, Yves; Jansson, Stefan; Hvidsten, Torgeir R; Street, Nathaniel R

    2015-12-01

    Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight. PMID:26192091

  7. Structures and stability of metal-doped GenM (n = 9, 10) clusters

    DOE PAGESBeta

    Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua; Zhao, Li-Zhen; Zang, Qing-Jun; Wang, C. Z.; Ho, K. M.

    2015-06-26

    The lowest-energy structures of neutral and cationic Ge nM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge9 and Ge10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Gen clusters. However, the neutral and cationic FeGe9,10,MnGe9,10 and Ge10Al are cage-like with the metal atom encapsulated inside. Suchmore »cage-like transition metal doped Gen clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge9,10Fe and Ge9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.« less

  8. What happens when someone talks in public to an audience they know to be entirely computer gen-

    E-print Network

    Slater, Mel

    designed a virtual public speaking scenario, followed by an experimental study. In this work we wanted compared to more general social interactions. A public speaking scenario involves specific stylizedWhat happens when someone talks in public to an audience they know to be entirely computer gen

  9. 327USDA Forest Service Gen.Tech. Rep. PSW-GTR-160. 1997. The Influence of Cattle Grazing on

    E-print Network

    327USDA Forest Service Gen.Tech. Rep. PSW-GTR-160. 1997. The Influence of Cattle Grazing of grazing leads to disappearance of squirrels. I compared moderate cattle grazing and grazing removal year-round by cattle but had not been grazed for 3 years before the study because of an extended

  10. USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 49 Effects of Wildfire on In-Channel Woody

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 49 Effects of Wildfire on In-Channel Woody Management of in-channel woody debris after wildfire is controversial. Post-fire increases in stream after wildfire in the Sierra Nevada is scant. Changes in debris frequency, mobility, volume, aggregation

  11. 553USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. The Effect of Low Oxygen Stress on

    E-print Network

    profile. An ODR below 0.2 corresponds to very low soil oxygen concentrations in clayey soils, i.e. 0553USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. The Effect of Low Oxygen Stress disease was quantified in cork oak (Quercus suber L.) roots subjected to low oxygen (hypoxia) stress

  12. USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 319 Summer and Fall Use of Logging Residue

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 319 Summer and Fall Use of Logging Residue Abstract Female short-tailed weasels (Mustela erminea) used piles of logging residue more than expected and used areas without logging residue less than expected when they were in 3-year- old regenerating aspen

  13. USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. 115 Forest Stand Structure and Development

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. 115 Forest Stand Structure and Development: Implications for Forest Management1 Kevin L. O'Hara2 A general premise of forest managers is that modern to these disturbances. An understanding of forest stand dynamics is therefore a prerequisite to sound forest management

  14. USDA Forest Service Gen. Tech. Rep. PSW-GTR-203. 2006. 121 Free Selection: A Silvicultural Option1

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-203. 2006. 121 Free Selection: A Silvicultural Option1 Russell T. Graham,2 Theresa B. Jain,2 and Jonathan Sandquist3 Abstract Forest management objectives to the challenge by supplying silvicultural methods and systems to produce desired stand and forest structures

  15. USDA Forest Service Gen. Tech. Rep. RMRS-GTR-42-vol. 3. 2012 157 Effects of Fire on Intangible Cultural

    E-print Network

    USDA Forest Service Gen. Tech. Rep. RMRS-GTR-42-vol. 3. 2012 157 Chapter 8: Effects of Fire in western forests as management priorities. The Policy, its 2001 revision,the2003HealthyForests remain the driving issue in forest management in the United States for the foreseeable future (Franklin

  16. Efforts to identify wildlife reservoirs for tick-borne patho-gens are frequently limited by poor understanding of tick

    E-print Network

    Allan, Brian

    Efforts to identify wildlife reservoirs for tick-borne patho- gens are frequently limited by poor. To identify reservoir hosts for lone star tick (Amblyomma americanum)­associated pathogens, we used a novel infection rates, our results confirm that the white-tailed deer (Odocoileus virginianus) is a reservoir host

  17. USDA Forest Service Gen. Tech. Rep. PSW-GTR-203. 2007. 193 Effects of Alternative Treatments on Canopy

    E-print Network

    ) · Douglas-fir (DF) · lodgepole pine (LP) · Sierra Nevada mixed conifer (SNMC) The previous canopy fuel study thinning treatments. The ponderosa-pine/Douglas-fir stand, with its significant understory component Service Gen. Tech. Rep. PSW-GTR-203. 2007.194 · ponderosa pine/Douglas-fir (PPDF) · ponderosa pine (PP

  18. USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 155 The Role of Disturbance in Creating Dead

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 155 The Role of Disturbance in Creating Dead and eventual conversion of standing dead to down logs, along with new seedling establishment, can result from of large insect outbreaks and the dynamics of dead wood in these mixed conifer stands. Introduction

  19. USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 679 Forest Management and the Dead Wood

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 679 Forest Management and the Dead Wood. These forest restoration treatments will affect the availability of dead wood to wildlife (e.g., prescribed fires may consume dead wood, forest operations may create snags and logs). I live- trapped small mammals

  20. USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 535 Regional Patterns of Dead Wood in

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 535 Regional Patterns of Dead Wood regional patterns of variation in dead wood across 20 million ha of upland forests of all ownerships plots. Current patterns of dead wood are highly variable and complex. The strongest differences were

  1. Evaluation of Mixed-Mode Data-Link Communications for NextGen 4DT and Equivalent Visual Surface Operations

    NASA Technical Reports Server (NTRS)

    Prinzel, Lawrence J., III; Shelton, Kevin J.; Jones, Denise R.; Allamandola, Angela S.; Arthur, Jarvis, J., III; Bailey, Randall E.

    2010-01-01

    By 2025, U.S. air traffic is predicted to increase 3-fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a revolutionary new concept has been proposed for U.S. aviation operations, termed the Next Generation Air Transportation System or NextGen. Many key capabilities are being identified to enable NextGen, including the use of data-link communications. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen. The paper describes simulation research examining data-link communications during 4DT and equivalent visual surface operations.

  2. USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 193 Distribution Patterns of Birds Associated

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 193 Distribution Patterns of Birds Associated with Snags in Natural and Managed Eastern Boreal Forests1 Pierre Drapeau,2 Antoine Nappi,2 Jean-François Giroux,2 Alain Leduc,2 and Jean-Pierre Savard3 Abstract In boreal forests, several bird species use

  3. 65USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Soil Characteristics of Blue Oak and

    E-print Network

    65USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Soil Characteristics of Blue Oak and Coast Live Oak Ecosystems1 Denise E. Downie2 Ronald D. Taskey2 Abstract: In northern San Luis Obispo County, California, soils associated with blue oaks (Quercus douglasii) are slightly more acidic, have finer textures

  4. 147USDAForestServiceGen.Tech.Rep.PSW-GTR-160.1997. Stand-Level Status of Blue Oak Sapling

    E-print Network

    147USDAForestServiceGen.Tech.Rep.PSW-GTR-160.1997. Stand-Level Status of Blue Oak Sapling assessed blue oak (Quercus douglasii) sapling recruitment and regeneration at 15 locations distributed throughout the range of blue oak. Overall, 15.3 percent of the 1500 plots surveyed contained blue oak

  5. USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 171 The Value of Coarse Woody Debris to

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 171 The Value of Coarse Woody Debris, and reptiles use coarse woody debris (i.e., standing and downed dead wood) for nesting, roosting, foraging habitat for amphibians and reptiles. Introduction Coarse woody debris, which is defined as standing dead

  6. JENUFA GEN. NOV.: A NEW GENUS OF COCCOID GREEN ALGAE (CHLOROPHYCEAE, INCERTAE SEDIS) PREVIOUSLY RECORDED BY ENVIRONMENTAL SEQUENCING1

    E-print Network

    JENUFA GEN. NOV.: A NEW GENUS OF COCCOID GREEN ALGAE (CHLOROPHYCEAE, INCERTAE SEDIS) PREVIOUSLY of unicellular green algae from algal biofilms growing on tree bark in a Southeast Asian tropical rainforest: AU, approximately unbiased; BBM, Bold basal medium; CAUP, Culture Collection of algae at Charles

  7. USDA Forest Service Gen. Tech. Rep. PSW-GTR-203. 2007. 109 Silviculture for the 21st

    E-print Network

    . Across the National Forest System, on other public lands, and increasingly on private lands as well that proposes to stop all logging in National Forests. And, in a clever response to working within the systemUSDA Forest Service Gen. Tech. Rep. PSW-GTR-203. 2007. 109 Silviculture for the 21st Century

  8. Gen Green: Changes in Australian Apprentices' and Trainees' Experience of Skills and Sustainability from 2008 to 2011

    ERIC Educational Resources Information Center

    Sack, Fabian

    2012-01-01

    The Gen Green research in 2008 and 2011 indicates that skills for sustainability public policy and business initiatives are having an impact, but that young skilled Australians' high level of interest in sustainability skills is confounded by a lack of guidance and incentives from employers, the market and educators. The research indicates that,…

  9. Modulation of the metabolic response to an endotoxin challenge in Brahman heifers through OmniGen-AF supplementation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study examined the effect of feeding OmniGen-AF (OG; Prince Agri Products) on the metabolic response of newly-weaned heifers to an endotoxin (lipopolysaccharide; LPS) challenge. Brahman heifers (n=24; 183±5 kilograms) from the Texas AgriLife Research Center in Overton, TX, were separated into 2...

  10. YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps

    PubMed Central

    Batesole, Keith; Wimalanathan, Kokulapalan; Liu, Lin; Zhang, Fan; Echt, Craig S.; Liang, Chun

    2014-01-01

    Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are uploaded, either publically or privately, as long as they follow our template which is available in several standard file formats. Data is parsed and loaded into MySQL relational database to be displayed and compared against users' genetic maps or other public data available on YouGenMap. With the highly interactive GUIs, all public data on YouGenMap are maps available for visualization, comparison, search, filtration and download. YouGenMap web tool is available on the website (http://conifergdb.miamioh.edu/yougenmap) with the source-code repository at (http://sourceforge.net/projects/yougenmap/?source=directory). PMID:25009553

  11. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 83 Breeding and Natal Dispersal, Nest Habitat Loss and

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 83 Breeding and Natal Dispersal, Nest Habitat 95825 Abstract: Evidence of breeding and natal dispersal in alcids is typically provided in consecutive breeding seasons, breeding site fidelity (birds breeding in the same nest as the previous year

  12. 75 FR 5780 - Green Borders Geothermal, LLC, Complainant, v. Terra-Gen Dixie Valley, LLC, Respondent; Notice of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-04

    ... From the Federal Register Online via the Government Printing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Green Borders Geothermal, LLC, Complainant, v. Terra-Gen Dixie Valley, LLC, Respondent; Notice of Complaint January 28, 2010. Take notice that on January 25, 2010, Green Borders Geothermal, LLC (Green Borders) filed...

  13. USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. 47 Response of Sierra Nevada Vegetation and Fire

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. 47 Response of Sierra Nevada Vegetation within forested communities of the Sierra Nevada has had a long history, initiated by the great-term changes--those caused by movements of the Earth's crust, such as the rise of the Sierra Nevada itself

  14. USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. v Introduction to the Sierra Nevada Science

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. v Introduction to the Sierra Nevada Science challenging. The complex and vexing land and resource management issues in the Sierra Nevada that require that land and resource managers must now address. The Sierra Nevada ecoregion is famous for its vast forests

  15. USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. 65 Fire in the Sierra Nevada1

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. 65 Fire in the Sierra Nevada1 Carl N for long-term functioning of Sierra Nevada ecosystems and as one of the greatest threats to human and natural resources (SNEP 1996a). Fire has shaped the terrestrial ecosystems of the Sierra Nevada

  16. USDA Forest Service Gen. Tech. Rep. PSW-GTR 193. 2004. i Proceedings for the Sierra Nevada Science

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR 193. 2004. i Proceedings for the Sierra Nevada Science and Policy in Sierra Nevada 1 Keynote 7 Session 1 ­ Climate and Landscape Change over Time 23 Session of 21st-century Climate Change and Watershed Responses in the Sierra Nevada 43 Michael D. Dettinger

  17. USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. 167 Biodiversity in the Sierra Nevada1

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. 167 Biodiversity in the Sierra Nevada1 Dennis D. Murphy,2 Erica Fleishman,3 and Peter A. Stine4 The earliest explorers of the Sierra Nevada was an especially rich assemblage of plants and animals, it was not until many decades later that the Sierra Nevada

  18. 139USDA Forest Service Gen. Tech. Rep. PSW-GTR-158. 1995. The Role of Fire in Ecosystem Management1

    E-print Network

    139USDA Forest Service Gen. Tech. Rep. PSW-GTR-158. 1995. The Role of Fire in Ecosystem Management1 Jerry T. Williams2 Abstract: USDA Forest Service management practices have sig- nificantly changed. Past. These changes have important implications for the agency's wildland fire manag- ers. This paper describes

  19. 11USDA Forest Service Gen. Tech. Rep. PSW-GTR-158. 1995. suppression on fuel accumulations. A program to improve

    E-print Network

    11USDA Forest Service Gen. Tech. Rep. PSW-GTR-158. 1995. suppression on fuel accumulations until USDA Forest Service researchers concluded that light burning was ineffective, impractical forest- ers about the benefits of prescribed fires. These field days became the basis for several

  20. YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps.

    PubMed

    Batesole, Keith; Wimalanathan, Kokulapalan; Liu, Lin; Zhang, Fan; Echt, Craig S; Liang, Chun

    2014-01-01

    Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are uploaded, either publically or privately, as long as they follow our template which is available in several standard file formats. Data is parsed and loaded into MySQL relational database to be displayed and compared against users' genetic maps or other public data available on YouGenMap. With the highly interactive GUIs, all public data on YouGenMap are maps available for visualization, comparison, search, filtration and download. YouGenMap web tool is available on the website (http://conifergdb.miamioh.edu/yougenmap) with the source-code repository at (http://sourceforge.net/projects/yougenmap/?source=directory). PMID:25009553

  1. 465USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. TreeVolume Equations for 10 Urban

    E-print Network

    465USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. TreeVolume Equations for 10 Urban Species-phase urban forest utilization project at California Polytechnic State University, San Luis Obispo. Selected samples of 10 urban species were carefully measured in order to develop tree volume equations

  2. 365USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Characteristics of Red-tailed Hawk

    E-print Network

    365USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Characteristics of Red-tailed Hawk Nest Abstract: Characteristics of nest sites of red-tailed hawks (Buteo jamaicensis) have not been described red-tailed hawk nests in oak woodlands in San Luis Obispo and Monterey Counties, California. We

  3. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 141 Inland Habitat Suitability for the Marbled Murrelet in

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 141 Inland Habitat Suitability for the Marbled Marbled Murrelet ground nests had been found (Day and others 1983). Since then, three tree nests have been of Marbled Murrelets (Day and others 1983). Therefore, it was unclear how important ground nesting

  4. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 271 Mortality of Marbled Murrelets in Gill Nets in North America

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 271 Chapter 27 Mortality of Marbled Murrelets: Mortality of Marbled Murrelets (Brachyramphus marmoratus) due to accidental capture in gill nets is one the impacts of gill-net mortality on the Marbled Murrelet (Brachyramphus marmoratus) (Carter and Morrison 1992

  5. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 177 A Landscape-Level Analysis of Marbled Murrelet Habitat in

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 177 A Landscape-Level Analysis of Marbled: Relationships between landscape-level patterns of for- est cover and occupancy by Marbled Murrelets in the state of Marbled Murrelet habitat selection proceeded at two scales. A broad scale analysis within major river

  6. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 295 Abstract: About 45,000-50,000 Marbled Murrelets (Brachyramphus

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 295 Abstract: About 45,000-50,000 Marbled in the population size of Marbled Murrelets and also in complexity of marine habitats used by these birds of the Marbled Murrelet obtained largely from boat surveys. Abundance and Distribution Regional and Range

  7. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 3 Ecology and Conservation of the Marbled Murrelet in

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 3 Ecology and Conservation of the Marbled4 Chapter 1 Abstract: Over the past decade, the Marbled Murrelet has become a focus of much Service in February 1993. In order to aid the various agencies with management, the Marbled Murrelet

  8. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 257 Pollution and Fishing Threats to Marbled Murrelets

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 257 Pollution and Fishing Threats to Marbled Murrelets D. Michael Fry1 Abstract: The principal pollutant threats to Marbled Murrelets are chlorinated and incineration product after burning of clearcut slash piles. Within the range of Marbled Murrelets, PCDD

  9. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 371 Productivity of Marbled Murrelets in California from

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 371 Chapter 35 Productivity of Marbled Murrelets an intensive survey method in 1993 to identify juvenile Marbled Murrelets (Brachyramphus marmoratus) at sea a demographic model of any species is a measure of that species' productivity. In the case of the Marbled

  10. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 261 Mortality of Marbled Murrelets Due to Oil Pollution

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 261 Mortality of Marbled Murrelets Due to Oil Pollution in North America Harry R. Carter1 Katherine J. Kuletz2 Abstract: Mortality of Marbled Murrelets pollution poses a significant threat to Marbled Murrelets (Brachyramphus marmoratus) in Alaska, British

  11. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 223 Marbled Murrelet Food Habits and Prey Ecology

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 223 Marbled Murrelet Food Habits and Prey Ecology Esther E. Burkett1 Abstract: Information on food habits of the Marbled Murrelet (Brachyramphus with El Niño events, could cause population declines and even extirpation. An understanding of Marbled

  12. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 23 The Asian Race of the Marbled Murrelet

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 23 The Asian Race of the Marbled Murrelet Nikolai B. Konyukhov1 Alexander S. Kitaysky2 Figure 1--Distribution of the Asian race of the Marbled. Methods In order to collect data on the distribution of the Marbled Murrelet in the Russian Far East

  13. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 327 Abundance and Distribution of Marbled Murrelets in Oregon

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 327 Abundance and Distribution of Marbled Abstract: To determine the abundance and distribution of Marbled Murrelets, aerial surveys of the Oregon and distribution is an important element in the conservation management of the Marbled Murrelet (Brachyramphus

  14. USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 257 The Pileated Woodpecker as a Keystone

    E-print Network

    categories of keystone species were described by Mills and others (1993), including keystone predators, preyUSDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 257 The Pileated Woodpecker as a Keystone that the pileated woodpecker (Dryocopus pileatus) is a keystone habitat modifier in the Pacific Northwest

  15. HAMULONEMA GEN. NOV. FOR OSTERTAGIA KENYENSIS AND TELADORSAGIA HAMATA IN THE OSTERTAGIINE FAUNA (NEMATODA: TRICHOSTRONGYLOIDEA) FROM AFRICAN UNGULATES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    : Hamulonema gen. nov. is proposed for Teladorsagia hamata and Ostertagia kenyensis in the ostertagiine nematode fauna found in artiodactyl hosts from Africa. Monomorphic species representing this genus are characterized by a bilaterally symmetrical and parallel synlophe in males and females, a 2-...

  16. 109USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Patterns and Processes of Adaptation

    E-print Network

    109USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Patterns and Processes of Adaptation suggest local scale adaptation. Differences among maternal families in survival and growth were that natural selection has resulted in the formation of genetically differentiated populations adapted to local

  17. USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 369 Assemblages of Vascular Plants on Logs

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 369 Assemblages of Vascular Plants on Logs and wildfire stands. Logs and stumps were colonized by a significantly different assemblage of vascular plants were similar. However, as dead wood decayed, assemblages of vascular plants diverged and became more

  18. 77 FR 52352 - Notice of Intent To Prepare an Environmental Impact Statement for the Rio Mesa Gen-Tie Project...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-29

    ... Gen-Tie Project and Possible Land Use Plan Amendment, Riverside County, CA AGENCY: Bureau of Land..., special management areas, land use, noise, paleontological resources, public health, socioeconomic, soils.... If a land use plan amendment is necessary, the BLM will integrate the land use planning process...

  19. WordGen: a tool for word selection and nonword generation in Dutch, English, German, and French.

    PubMed

    Duyck, Wouter; Desmet, Timothy; Verbeke, Lieven P C; Brysbaert, Marc

    2004-08-01

    WordGen is an easy-to-use program that uses the CELEX and Lexique lexical databases for word selection and nonword generation in Dutch, English, German, and French. Items can be generated in these four languages, specifying any combination of seven linguistic constraints: number of letters, neighborhood size, frequency, summated position-nonspecific bigram frequency, minimum position-nonspecific bigram f requency, position-specific frequency of the initial and final bigram, and orthographic relatedness. The program also has a module to calculate the respective values of these variables for items that have already been constructed, either with the program or taken from earlier studies. Stimulus queries can be entered through WordGen's graphical user interface or by means of batch files. WordGen is especially useful for (1) Dutch and German item generation, because no such stimulus-selection tool exists for these languages, (2) the generation of nonwords for all four languages, because our program has some important advantages over previous nonword generation approaches, and (3) psycholinguistic experiments on bilingualism, because the possibility of using the same tool for different languages increases the cross-linguistic comparability of the generated item lists. WordGen is free and available at http://expsy.ugent.be/wordgen.htm. PMID:15641437

  20. USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 489 The Number and Composition of Snags in

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 489 The Number and Composition of Snags bordering deciduous stands and now is a well regenerating tree species. Spruce regeneration slowed within these changes reflect snag characteristics and composition. Introduction Most of the lowland forests

  1. Page 1 of 5 GenMAPP Gene Database for Salmonella typhimurium (strain ATCC 700720 / SGSC1412 / LT2)

    E-print Network

    Dahlquist, Kam D.

    Page 1 of 5 GenMAPP Gene Database for Salmonella typhimurium (strain ATCC 700720 / SGSC1412 / LT2MAPP requires a separate Gene Database for each species. This ReadMe describes a Gene Database for Salmonella. Gene Database Specifications a. Gene ID Systems This Salmonella typhimurium Gene Database is Uni

  2. USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. 149 Assessing Cumulative Watershed Effects in the

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. 149 Assessing Cumulative Watershed Effects and time. Land and aquatic resource managers are particularly concerned with cumulative watershed effects quality, channel morphology, and aquatic ecosystems at the watershed scale (Reid 1993). CWEs are a class

  3. A review of Chinese tribe Achilini (Hemiptera: Fulgoromorpha: Achilidae),
    with descriptions of Paracatonidia webbeda gen. & sp. nov.

    PubMed

    Long, Jian-Kun; Yang, Lin; Chen, Xiang-Sheng

    2015-01-01

    Planthoppers of the tribe Achilini (Hemiptera: Fulgoromorpha: Achilidae) from China, are reviewed. A key to the three genera of Chinese Achilini is given. A new genus and species of the tribe from southwestern China: Paracatonidia webbeda gen. & sp. nov., is described. A new genus and species record for China, Cixidia kasparyani Anufriev, is also given. PMID:26701421

  4. 115USDA Forest Service Gen. Tech. Rep. PSW-GTR-158. 1995. Regional Approaches to Urban Interface Problems

    E-print Network

    , command post locations, staging areas, designated radio frequencies, helicopter landing zones, evacuation115USDA Forest Service Gen. Tech. Rep. PSW-GTR-158. 1995. Regional Approaches to Urban Interface that want to develop a pre-suppression plan by designating the high-risk areas in the community

  5. OmniGen-AF supplementation modulated the physiological and acute phase responses of Brahman heifers to an endotoxin challenge

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study examined the effect of feeding OmniGen-AF (OG; Prince Agri Products) on the physiological and acute phase responses (APR) of newly-weaned heifers to an endotoxin (lipopolysaccharide; LPS) challenge. Brahman heifers (n=24; 183±5 kilograms) from the Texas AgriLife Research Center in Overton...

  6. Page 1 of 4 GenMAPP Gene Database for Vibrio cholerae O1 biovar El Tor str. N16961

    E-print Network

    Dahlquist, Kam D.

    Page 1 of 4 GenMAPP Gene Database for Vibrio cholerae O1 biovar El Tor str. N16961 Vc. This ReadMe describes a Gene Database for Vibrio cholerae O1 biovar El Tor str. N16961 that was built Specifications a. Gene ID Systems This Vibrio cholerae Gene Database is UniProt-centric in that the main data

  7. Page 1 of 4 GenMAPP Gene Database for Vibrio cholerae O1 biovar El Tor str. N16961

    E-print Network

    Dahlquist, Kam D.

    Page 1 of 4 GenMAPP Gene Database for Vibrio cholerae O1 biovar El Tor str. N16961 VcMAPP requires a separate Gene Database for each species. This ReadMe describes a Gene Database for Vibrio Specifications a. Gene ID Systems This Vibrio cholerae Gene Database is UniProt-centric in that the main data

  8. 1.Phys. A: Math. Gen. 27 (1994) 2687-2708. Printed in the UK On the 3D Isingspin glass

    E-print Network

    Ritort, Felix

    1994-01-01

    1.Phys. A: Math. Gen. 27 (1994) 2687-2708. Printed in the UK On the 3D Isingspin glass Enzo, 08028 Barcelona. Spain Received 21 October 1993 Abstract We study the 3D king spin glass with i l.T transition or by a T =0 singularityof an unusual type. 1. Introduction Three-dimensional spin glasses [1

  9. SkelGen: a general tool for structure-based de novo ligand design.

    PubMed

    Dean, Philip M; Firth-Clark, Stuart; Harris, William; Kirton, Stewart B; Todorov, Nikolay P

    2006-07-01

    The recent lapse in productivity in the pharmaceutical industry has facilitated the emergence of experimental and in silico structure-based design methodologies, based on identification of biologically active low molecular weight fragments that can be exploited to produce potential drug candidates with diverse chemistries. SkelGen, an in silico example of this methodology, is reviewed. The ability of this algorithm to identify chemically diverse low molecular weight fragments that would potentially bind to DNA gyrase is recounted, as is the first purely de novo structure-based design of five compounds that show at least micromolar activity against the estrogen receptor. The ability of the algorithm to incorporate partial protein flexibility during its design of compounds to the estrogen receptor is discussed, and an opinion as to the near and long-term futures for de novo design algorithms is expressed. PMID:23495800

  10. Reclassification of Saccharomycodes sinensis, Proposal of Yueomyces sinensis gen. nov., comb. nov. within Saccharomycetaceae (Saccharomycetales, Saccharomycotina)

    PubMed Central

    Wang, Long; Groenewald, Marizeth; Wang, Qi-Ming; Boekhout, Teun

    2015-01-01

    The phylogenetic position of Saccharomycodes sinensis has been debated by yeast taxonomists. In this study, a multigene phylogenetic analysis based on four regions, namely the 18S ribosomal DNA (rDNA), the D1/D2 domains of the 26S rDNA, the second largest subunit of RNA polymerase II gene (RPB2) and translation elongation factor 1-? gene (EF1-?), were performed to address the phylogenetic placement of S. sinensis. Our result indicated that S. sinensis belongs to Saccharomycetaceae instead of Saccharomycodaceae, and forms a single species lineage divergent from the other genera within Saccharomycetaceae. Yueomyces gen. nov. (MycoBank No. MB 811648) is proposed in the Saccharomycetaceae with Y. sinensis comb. nov. (MycoBank No. MB 811649, type strain CGMCC 2.01395T = IFO 10111T = CBS 7075T) as the type species. PMID:26375944

  11. Multimodal information Management: Evaluation of Auditory and Haptic Cues for NextGen Communication Displays

    NASA Technical Reports Server (NTRS)

    Begault, Durand R.; Bittner, Rachel M.; Anderson, Mark R.

    2012-01-01

    Auditory communication displays within the NextGen data link system may use multiple synthetic speech messages replacing traditional ATC and company communications. The design of an interface for selecting amongst multiple incoming messages can impact both performance (time to select, audit and release a message) and preference. Two design factors were evaluated: physical pressure-sensitive switches versus flat panel "virtual switches", and the presence or absence of auditory feedback from switch contact. Performance with stimuli using physical switches was 1.2 s faster than virtual switches (2.0 s vs. 3.2 s); auditory feedback provided a 0.54 s performance advantage (2.33 s vs. 2.87 s). There was no interaction between these variables. Preference data were highly correlated with performance.

  12. Uktena riparia n. gen., n. sp. (Annelida, Clitellata, Lumbriculidae), a new spermatophore-producing oligochaete.

    PubMed

    Fend, Steven V; Rodriguez, Pilar; Lenat, David R

    2015-01-01

    Uktena riparia n. gen., n. sp. has been collected in hyporheic habitats at several sites in North Carolina, southeastern USA. The genus is defined by unusual characters related to reproductive structures, including the formation of encapsulated spermatophores for sperm transfer and large bundles of genital chaetae, both previously unknown in the Lumbriculidae. The simultaneous occurrence of both spermatophores and spermathecae is rare in the microdrile oligochaetes. Uktena spermatophores appear more similar to those reported in leeches than to those in other microdrile oligochaete families. Possible synapomorphies associating Uktena with the genera Kincaidiana and Guestphalinus include a filiform, ringed proboscis, a forward shift of reproductive organs relative to the usual position in the family, and spermathecae in the atrial segment. The new species adds to the already diverse, endemic lumbriculid fauna of the North Carolina Sandhills ecoregion. PMID:26250281

  13. The haemosporidian parasites of bats with description of Sprattiella alecto gen. nov., sp. nov.

    PubMed Central

    Landau, I.; Chavatte, J.M.; Karadjian, G.; Chabaud, A.; Beveridge, I.

    2012-01-01

    Four species of Haemoproteidae were found in Pteropus alecto Temminck, 1837 in Queensland, Australia: i) Johnsprentia copemani, Landau et al., 2012; ii) Sprattiella alecto gen. nov., sp. nov., characterised by schizonts in the renal vessels; iii) Hepatocystis levinei, Landau et al., 1985, originally described from Pteropus poliocephalus Temminck, 1825 and, experimentally from Culicoides nubeculosus and found in this new host and for which features of the hepatic schizonts are reported; iv) gametocytes of Hepatocystis sp. which are illustrated but cannot be assigned to a known species. A tentative interpretation of phylogenetic characters of haemosporidians of bats is provided from the morphology of the gametocytes and localisation of the tissue stages with respect to recent data on the phylogeny of bats. PMID:22550624

  14. IceCube-Gen2: A Vision for the Future of Neutrino Astronomy in Antarctica

    E-print Network

    IceCube-Gen2 Collaboration; :; M. G. Aartsen; M. Ackermann; J. Adams; J. A. Aguilar; M. Ahlers; M. Ahrens; D. Altmann; T. Anderson; G. Anton; C. Arguelles; T. C. Arlen; J. Auffenberg; S. Axani; X. Bai; I. Bartos; S. W. Barwick; V. Baum; R. Bay; J. J. Beatty; J. Becker Tjus; K. -H. Becker; S. BenZvi; P. Berghaus; D. Berley; E. Bernardini; A. Bernhard; D. Z. Besson; G. Binder; D. Bindig; M. Bissok; E. Blaufuss; J. Blumenthal; D. J. Boersma; C. Bohm; F. Bos; D. Bose; S. Böser; O. Botner; L. Brayeur; H. -P. Bretz; A. M. Brown; N. Buzinsky; J. Casey; M. Casier; E. Cheung; D. Chirkin; A. Christov; B. Christy; K. Clark; L. Classen; F. Clevermann; S. Coenders; G. H. Collin; J. M. Conrad; D. F. Cowen; A. H. Cruz Silva; J. Daughhetee; J. C. Davis; M. Day; J. P. A. M. de André; C. De Clercq; S. De Ridder; P. Desiati; K. D. de Vries; M. de With; T. DeYoung; J. C. Dí andaz-Vélez; M. Dunkman; R. Eagan; B. Eberhardt; T. Ehrhardt; B. Eichmann; J. Eisch; S. Euler; J. J. Evans; P. A. Evenson; O. Fadiran; A. R. Fazely; A. Fedynitch; J. Feintzeig; J. Felde; K. Filimonov; C. Finley; T. Fischer-Wasels; S. Flis; K. Frantzen; T. Fuchs; T. K. Gaisser; R. Gaior; J. Gallagher; L. Gerhardt; D. Gier; L. Gladstone; T. Glüsenkamp; A. Goldschmidt; G. Golup; J. G. Gonzalez; J. A. Goodman; D. Góra; D. Grant; P. Gretskov; J. C. Groh; A. Groß; C. Ha; C. Haack; A. Haj Ismail; P. Hallen; A. Hallgren; F. Halzen; K. Hanson; J. Haugen; D. Hebecker; D. Heereman; D. Heinen; K. Helbing; R. Hellauer; D. Hellwig; S. Hickford; J. Hignight; G. C. Hill; K. D. Hoffman; R. Hoffmann; A. Homeier; K. Hoshina; F. Huang; W. Huelsnitz; P. O. Hulth; K. Hultqvist; A. Ishihara; E. Jacobi; J. Jacobsen; G. S. Japaridze; K. Jero; O. Jlelati; B. J. P. Jones; M. Jurkovic; O. Kalekin; A. Kappes; T. Karg; A. Karle; T. Katori; U. F. Katz; M. Kauer; A. Keivani; J. L. Kelley; A. Kheirandish; J. Kiryluk; J. Kläs; S. R. Klein; J. -H. Köhne; G. Kohnen; H. Kolanoski; A. Koob; L. Köpke; C. Kopper; S. Kopper; D. J. Koskinen; M. Kowalski; C. B. Krauss; A. Kriesten; K. Krings; G. Kroll; M. Kroll; J. Kunnen; N. Kurahashi; T. Kuwabara; M. Labare; J. L. Lanfranchi; D. T. Larsen; M. J. Larson; M. Lesiak-Bzdak; M. Leuermann; J. LoSecco; J. Lünemann; J. Madsen; G. Maggi; K. B. M. Mahn; S. Marka; Z. Marka; R. Maruyama; K. Mase; H. S. Matis; R. Maunu; F. McNally; K. Meagher; M. Medici; A. Meli; T. Meures; S. Miarecki; E. Middell; E. Middlemas; N. Milke; J. Miller; L. Mohrmann; T. Montaruli; R. W. Moore; R. Morse; R. Nahnhauer; U. Naumann; H. Niederhausen; S. C. Nowicki; D. R. Nygren; A. Obertacke; S. Odrowski; A. Olivas; A. Omairat; A. O'Murchadha; T. Palczewski; L. Paul; Ö. Penek; J. A. Pepper; C. Pérez de los Heros; C. Pfendner; D. Pieloth; E. Pinat; J. L. Pinfold; J. Posselt; P. B. Price; G. T. Przybylski; J. Pütz; M. Quinnan; L. Rädel; M. Rameez; K. Rawlins; P. Redl; I. Rees; R. Reimann; M. Relich; E. Resconi; W. Rhode; M. Richman; B. Riedel; S. Robertson; J. P. Rodrigues; M. Rongen; C. Rott; T. Ruhe; B. Ruzybayev; D. Ryckbosch; S. M. Saba; H. -G. Sander; J. Sandroos; P. Sandstrom; M. Santander; S. Sarkar; K. Schatto; F. Scheriau; T. Schmidt; M. Schmitz; S. Schoenen; S. Schöneberg; A. Schönwald; A. Schukraft; L. Schulte; O. Schulz; D. Seckel; Y. Sestayo; S. Seunarine; M. H. Shaevitz; R. Shanidze; M. W. E. Smith; D. Soldin; S. Söldner-Rembold; G. M. Spiczak; C. Spiering; M. Stamatikos; T. Stanev; N. A. Stanisha; A. Stasik; T. Stezelberger; R. G. Stokstad; A. Stöß andl; E. A. Strahler; R. Ström; N. L. Strotjohann; G. W. Sullivan; H. Taavola; I. Taboada; A. Taketa; A. Tamburro; H. K. M. Tanaka; A. Tepe; S. Ter-Antonyan; A. Terliuk; G. Teš; andi?; S. Tilav; P. A. Toale; M. N. Tobin; D. Tosi; M. Tselengidou; E. Unger; M. Usner; S. Vallecorsa; N. van Eijndhoven; J. Vandenbroucke; J. van Santen; S. Vanheule; M. Vehring; M. Voge; M. Vraeghe; C. Walck; M. Wallraff; Ch. Weaver; M. Wellons; C. Wendt; S. Westerhoff; B. J. Whelan; N. Whitehorn; C. Wichary; K. Wiebe; C. H. Wiebusch; D. R. Williams; H. Wissing; M. Wolf; T. R. Wood; K. Woschnagg; S. Wren; D. L. Xu; X. W. Xu; Y. Xu; J. P. Yanez; G. Yodh; S. Yoshida; P. Zarzhitsky; J. Ziemann; M. Zoll

    2014-12-18

    The recent observation by the IceCube neutrino observatory of an astrophysical flux of neutrinos represents the "first light" in the nascent field of neutrino astronomy. The observed diffuse neutrino flux seems to suggest a much larger level of hadronic activity in the non-thermal universe than previously thought and suggests a rich discovery potential for a larger neutrino observatory. This document presents a vision for an substantial expansion of the current IceCube detector, IceCube-Gen2, including the aim of instrumenting a $10\\,\\mathrm{km}^3$ volume of clear glacial ice at the South Pole to deliver substantial increases in the astrophysical neutrino sample for all flavors. A detector of this size would have a rich physics program with the goal to resolve the sources of these astrophysical neutrinos, discover GZK neutrinos, and be a leading observatory in future multi-messenger astronomy programs.

  15. Decay Heat Removal in GEN IV Gas-Cooled Fast Reactors

    DOE PAGESBeta

    Cheng, Lap-Yan; Wei, Thomas Y. C.

    2009-01-01

    The safety goal of the current designs of advanced high-temperature thermal gas-cooled reactors (HTRs) is that no core meltdown would occur in a depressurization event with a combination of concurrent safety system failures. This study focused on the analysis of passive decay heat removal (DHR) in a GEN IV direct-cycle gas-cooled fast reactor (GFR) which is based on the technology developments of the HTRs. Given the different criteria and design characteristics of the GFR, an approach different from that taken for the HTRs for passive DHR would have to be explored. Different design options based on maintaining core flow weremore »evaluated by performing transient analysis of a depressurization accident using the system code RELAP5-3D. The study also reviewed the conceptual design of autonomous systems for shutdown decay heat removal and recommends that future work in this area should be focused on the potential for Brayton cycle DHRs.« less

  16. NASA System-Level Design, Analysis and Simulation Tools Research on NextGen

    NASA Technical Reports Server (NTRS)

    Bardina, Jorge

    2011-01-01

    A review of the research accomplished in 2009 in the System-Level Design, Analysis and Simulation Tools (SLDAST) of the NASA's Airspace Systems Program is presented. This research thrust focuses on the integrated system-level assessment of component level innovations, concepts and technologies of the Next Generation Air Traffic System (NextGen) under research in the ASP program to enable the development of revolutionary improvements and modernization of the National Airspace System. The review includes the accomplishments on baseline research and the advancements on design studies and system-level assessment, including the cluster analysis as an annualization standard of the air traffic in the U.S. National Airspace, and the ACES-Air MIDAS integration for human-in-the-loop analyzes within the NAS air traffic simulation.

  17. Enhanced Vision for All-Weather Operations Under NextGen

    NASA Technical Reports Server (NTRS)

    Bailey, Randall E.; Kramer, Lynda J.; Williams, Steven P.; Bailey, Randall E.; Kramer, Lynda J.; Williams, Steven P.

    2010-01-01

    Recent research in Synthetic/Enhanced Vision technology is analyzed with respect to existing Category II/III performance and certification guidance. The goal is to start the development of performance-based vision systems technology requirements to support future all-weather operations and the NextGen goal of Equivalent Visual Operations. This work shows that existing criteria to operate in Category III weather and visibility are not directly applicable since, unlike today, the primary reference for maneuvering the airplane is based on what the pilot sees visually through the "vision system." New criteria are consequently needed. Several possible criteria are discussed, but more importantly, the factors associated with landing system performance using automatic and manual landings are delineated.

  18. Eremonidiopsis aggregata, gen. n., sp. n. from Cuba, the third West Indian Dioptinae (Lepidoptera, Notodontidae)

    PubMed Central

    Aguila, Rayner Núñez

    2013-01-01

    Abstract A new genus and species of Dioptinae (Lepidoptera, Noctuoidea, Notodontidae) is described from Cuba, this being the third taxon of the subfamily known from the West Indies. Eremonidiopsis aggregata, gen. n., sp. n., appears to be closely related to Eremonidia mirifica Rawlins & Miller from Hispaniola among members of the tribe Dioptini. Eremonidiopsis aggregata is known from two localities in the middle and western portions of the northeastern Cuban mountain range, Nipe–Sagua–Baracoa. The species inhabits low elevations (300–400 m) covered by lowland rainforest and sclerophyll rainforest. The six known specimens, all males, were part of small swarms flying near the top of an unidentified tree during the day at both collecting sites. These localities are included within protected areas, the “Pico Cristal” National Park in the West and the “Alexander von Humbolt” National Park in the East. PMID:24146561

  19. Life cycle of Schizochytriodinium calani nov. gen. nov. spec., a dinoflagellate parasitizing copepod eggs

    NASA Astrophysics Data System (ADS)

    Elbrächter, Malte

    1988-09-01

    During the Polarstern-cruise ARK IV/2 June 1987, in the Fram Strait, dinophytes parasitizing copepod eggs were observed. In the laboratory on board, vegetative reproduction was documented and re-infection of Calanus glacialis and C. hyperboreus eggs was experimentally established. During food uptake, a primary cyst produces successively several secondary cysts, all separating immediately after formation from the primary cyst. In every one of these free floating secondary cysts up to 256 dinospores are formed by palintomy. Re-infection only occurred after a “maturation time” of at least 2 days after formation of the dinospores. The life cycle is compared to that of other similar parasitic dinophyte genera: Apodinium Chatton, Chytriodinium Chatton, Dissodinium Klebs in Pascher and Myxodinium Cachon, Cachon & Bouquaheux. As the taxon under discussion does not fit in with any species or genus known so far, it is described as Schizochytriodinium calani nov. gen. nov. spec.

  20. A New Deep-branching Stramenopile, Platysulcus tardus gen. nov., sp. nov.

    PubMed

    Shiratori, Takashi; Nakayama, Takeshi; Ishida, Ken-ichiro

    2015-07-01

    A novel free-living heterotrophic stramenopile, Platysulcus tardus gen. nov., sp. nov. was isolated from sedimented detritus on a seaweed collected near the Ngeruktabel Island, Palau. P. tardus is a gliding flagellate with tubular mastigonemes on the anterior short flagellum and a wide, shallow ventral furrow. Although the flagellar apparatus of P. tardus is typical of stramenopiles, it shows novel ultrastructural combinations that are not applied to any groups of heterotrophic stramenopiles. Phylogenetic analysis using SSU rRNA genes revealed that P. tardus formed a clade with stramenopiles with high support. However, P. tardus did not form a subclade with any species or environmental sequences within the stramenopiles, and no close relative was suggested by the phylogenetic analysis. Therefore, we concluded that P. tardus should be treated as a new genus and species of stramenopiles and have proposed a new family, Platysulcidae fam. nov., for this phylogenetically distinct organism. PMID:26070192

  1. Microstructure stability of candidate stainless steels for Gen-IV SCWR fuel cladding application

    NASA Astrophysics Data System (ADS)

    Li, Jian; Zheng, W.; Penttilä, S.; Liu, P.; Woo, O. T.; Guzonas, D.

    2014-11-01

    In the past few years, significant progress has been made in materials selection for Gen-IV SCWR fuel cladding applications. Current studies indicate that austenite stainless steels such as 310H are promising candidates for in-core applications. Alloys in this group are promising for their corrosion resistance, SCC resistance, high temperature mechanical properties and creep resistance at temperatures up to 700 °C. However, one under-studied area of this alloy is the long-term microstructure stability under the proposed reactor operating condition. Unstable microstructure not only results in embrittlement but also has the potential to reduce their resistance to corrosion or stress-corrosion cracking. In this study, stainless steels 310H and 304H were tested for their SCWR corrosion resistance and microstructure stability.

  2. Combresomyces cornifer gen. sp. nov., an endophytic peronosporomycete in Lepidodendron from the Carboniferous of central France.

    PubMed

    Dotzler, Nora; Krings, Michael; Agerer, Reinhard; Galtier, Jean; Taylor, Thomas N

    2008-09-01

    Structurally preserved periderm of the lycophyte Lepidodendron rhodumnense from the Visean (Mississippian) of central France contains a peronosporomycete (Combresomyces cornifer gen. sp. nov.) that occurs in the form of pyriform to subglobose terminal oogonia. On the surface is a conspicuous ornamentation, which may have formed through condensation of a mucilaginous extra-oogonial wall secretion. Some oogonia contain thin-walled spherules, which may represent (walled) oospheres or spores of an endoparasitic fungus (?chytrid), whereas single, large spheres in the interior are interpreted as oospores. Antheridia adpressed to several of the specimens are clavate and paragynous. This discovery sheds light on the morphology and biology of peronosporomycetes in a terrestrial ecosystem some 330My ago. Although the organism occurs exclusively in the periderm of L. rhodumnense, it is not known whether it represents a symptomless endophyte, pathogen, or saprotroph. PMID:18692373

  3. Parablastomonas arctica gen. nov., sp. nov., isolated from high Arctic glacial till.

    PubMed

    Ren, Lvzhi; Chang, Xulu; Jiang, Fan; Kan, Wenjing; Qu, Zhihao; Qiu, Xia; Fang, Chengxiang; Peng, Fang

    2015-01-01

    A pale yellow, aerobic bacterium, strain M0-2(T), was isolated from a till sample. Its taxonomic position was investigated by using a polyphasic approach. Cells were Gram-stain-negative, rod-shaped and motile. Cells reproduced by budding or asymmetrical cell division. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M0-2(T) belonged to the family Sphingomonadaceae and was closely related to species of the genera Novosphingobium (96.4-92.0%) and Blastomonas (94.6%), Sphingopyxis witflariensis W-50(T) (94.0%), Sphingosinicella soli KSL-125(T) (93.6%) and Sphingomonas astaxanthinifaciens TDMA-17(T) (93.5%). Ubiquinone-10 (Q-10) was the predominant respiratory quinone. The major fatty acids were summed feature 8 (comprising C18:1?7c and/or C18:1?6c, 31.9%), summed feature 3 (comprising C16:1?7c and/or C16:1?6c, 19.8%) and C14:0 2-OH (8.9%). Sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine were the major polar lipids. Spermidine was the major polyamine observed in the cell. The genomic DNA G+C content was 47.5 mol%. On the basis of phylogenetic relationships and the low DNA G+C content compared with most other genera of the family Sphingomonadaceae, combined with phenotypic and chemotaxonomic data, strain M0-2(T) is considered to represent a novel species in a new genus in the family Sphingomonadaceae for which the name Parablastomonas arctica gen. nov., sp. nov. is proposed. The type strain of Parablastomonas arctica gen. nov., sp. nov. is M0-2(T) (?=CCTCC AB 2012968(T)?=?NRRL B-59110(T)). PMID:25336722

  4. AN EXPLORATION OF DIVERSITY AMONG THE OSTERTAGIINAE: AFRICANASTRONGYLUS BUCEROS GEN. NOV. ET SP. NOV. (NEMATODA: TRICHOSTRONGYLOIDEA) IN AFRICAN BUFFALO (SYNCERUS CAFFER).

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Abomasal nematodes (Ostertagiine: Trichostrongyloidea) representing a previously unrecognized genus and species are reported in African Buffalo (Syncerus caffer caffer) from Kenya, Uganda and South Africa. Africanastrongylus buceros gen. nov. et sp. nov. is characterized by a symmetrical tapering ...

  5. GenBank at Los Alamos: User manual, training guide, and reference manual for the OPEN LOOK[trademark] AWB

    SciTech Connect

    Reese, G.C.; Keen, G.M.; Gilna, P.; Cinkosky, M.J.

    1993-03-15

    The GenBank project at Los Alamos collects nucleotide sequence submissions from the biological research community. This work includes the processing of data received in several different forms as well as maintenance and quality control on those submissions. This manual explains the procedures involved in that work for both Los Alamos GenBank staff and off-site users. The GenBank database stores annotated DNA sequences. This manual contains the procedures for depositing these sequences into the database. There are two ways to do this. Either the sequence arrives at GenBank as a submission and is entered by the database staff or the sequence is directly entered by an off-site user. The Annotator's WorkBench (AWB), which is a database browsing and editing tool, is used in both cases. This manual is for GenBank staff and off-site users of the GenBank database at the Los Alamos National Laboratory. It contains an introduction and tutorials for AWB, as well as procedures for entering sequences either as submissions or as data directly deposited by an off-site user. Instructions for all of these are found in Chapters 2 through 4. The introduction to AWB is in Chapter 2. Instructions for submission handling are in Chapter 3. Instructions for entering sequence information are in Chapter 4. Off-site users should look at section 4.3 for instructions on entering a sequence. In addition, the manual describes various in-house curatorial tasks that are part of maintaining the database, as well as the procedures and conventions for annotating sequences. The procedures for annotation and review are in Chapters 5 and 6. The description of in-house curator's tasks is in Chapter 7. The appendices contain: Annotation conventions, two reference chapters on AWB and other utility programs, a complete list of all the forms, fields, and commands in AWB and descriptions of other (non-AWB) software utilities used by database staff.

  6. GenBank at Los Alamos: User manual, training guide, and reference manual for the ASCII AWB

    SciTech Connect

    Reese, G.C.; Keen, G.M.; Gilna, P.; Cinkosky, M.J.

    1993-03-15

    The GenBank project at Los Alamos collects nucleotide sequence submissions from the biological research community. This work includes the processing of data received in several different forms as well as maintenance and quality control on those submissions. This manual explains the procedures involved in that work for both Los Alamos GenBank staff and off-site users. The GenBank database stores annotated DNA sequences. This manual contains the procedures for depositing these sequences into the database. There are two ways to do this. Either the sequence arrives at GenBank as a submission and is entered by the database staff or the sequence is directly entered by an off-site user. The Annotator's WorkBench (AWB), which is a database browsing and editing tool, is used in both cases. This manual is for GenBank staff and off-site users of the GenBank database at the Los Alamos National Laboratory. It contains an introduction and tutorials for AWB, as well as procedures for entering sequences either as submissions or as data directly deposited by an off-site user. Instructions for all of these are found in Chapters 2 through 4. The introduction to AWB is in Chapter 2. Instructions for submission handling are in Chapter 3. Instructions for entering sequence information are in Chapter 4. Off-site users should look at section 4.3 for instructions on entering a sequence. In addition, the manual describes various in-house curatorial tasks that are part of maintaining the database, as well as the procedures and conventions for annotating sequences. The procedures for annotation and review are in Chapters 5 and 6. The description of in-house curator's tasks is in Chapter 7. The appendices contain: Annotation conventions, two reference chapters on AWB and other utility programs, a complete list of all the forms, fields, and commands in AWB and descriptions of other (non-AWB) software utilities used by database staff.

  7. Cleaning Supplies Manufacturer/Supplier Gen Peds GI ETC US CT MRI BI Ortho FCC Angio PET A33 Dry Airkem X

    E-print Network

    Cleaning Supplies Manufacturer/Supplier Gen Peds GI ETC US CT MRI BI Ortho FCC Angio PET NUC MED A\\MSDS.xls #12;Cleaning Supplies Manufacturer/Supplier Gen Peds GI ETC US CT MRI BI Ortho FCC Angio PET NUC MED Clean S.C. Johnson & Son, Inc. Sani-Cloth PDI X X X X X X X X X Skin Conditioner Aloe Vesta Skin Prep

  8. Koponenius gen. nov., a new genus of the millipede family Haplodesmidae from the Himalayas of India and Nepal (Diplopoda: Polydesmida).

    PubMed

    Golovatch, Sergei I; Vandenspiegel, Didier

    2014-01-01

    The first, apparently westernmost indigenous representatives of Haplodesmidae are reported, from the Himalayas of Nepal and India. Both new species belong to a new genus, Koponenius gen. nov., with K. unicornis sp. nov., the type species from Darjeeling District, NE India, and K. biramus sp. nov., from Nepal. The new genus is superficially very similar to Prosopodesmus Silvestri, 1910, most species of which seem to be native to tropical Australia, partly also to southern Japan. However, Koponenius gen. nov. is easily distinguished in showing only 19 body segments, a special ozopore formula (5, 7-18), 4 transverse rows of setigerous isostictic tubercles per postcollum metatergum, and a clearly helicoid, twisted prefemoral portion of the gonopod so that the seminal groove runs mostly laterally, not mesally.  PMID:25544626

  9. Hold your horSSEs: controlling structure-selective endonucleases MUS81 and Yen1/GEN1

    PubMed Central

    Blanco, Miguel G.; Matos, Joao

    2015-01-01

    Repair of DNA lesions through homologous recombination promotes the establishment of stable chromosomal interactions. Multiple helicases, topoisomerases and structure-selective endonucleases (SSEs) act upon recombining joint molecules (JMs) to disengage chromosomal connections and safeguard chromosome segregation. Recent studies on two conserved SSEs – MUS81 and Yen1/GEN1– uncovered multiple layers of regulation that operate to carefully tailor JM-processing according to specific cellular needs. Temporal restriction of SSE function imposes a hierarchy in pathway usage that ensures efficient JM-processing while minimizing reciprocal exchanges between the recombining DNAs. Whereas a conserved strategy of fine-tuning SSE functions exists in different model systems, the precise molecular mechanisms to implement it appear to be significantly different. Here, we summarize the current knowledge on the cellular switches that are in place to control MUS81 and Yen1/GEN1 functions. PMID:26284109

  10. Quisarctus yasumurai gen. et sp. nov. (Arthrotardigrada: Halechiniscidae) from a submarine cave, off Iejima, Ryukyu Islands, Japan.

    PubMed

    Fujimoto, Shinta

    2015-01-01

    Quisarctus yasumurai gen. et sp. nov. (Arthrotardigrada: Halechiniscidae) is described from the submarine cave 'Daidokutsu', off Iejima, Okinawa Islands, Ryukyu Islands, Japan. It is characterised by a cylindrical body, long primary clava and shorter lateral cirrus inserted on a common cirrophore, and simple digits of unequal lengths (without folds, peduncles, proximal pads, pretarsi, or wrinkles) that terminate in a sheathed, small, crescent-shaped claw with a minute calcar. Quisarctinae subfam. nov. is erected for this unique new genus. PMID:25947769

  11. Surface Map Traffic Intent Displays and Net-Centric Data-link Communications for NextGen

    NASA Technical Reports Server (NTRS)

    Shelton, Kevin J.; Prinzel, Lawrence J., III; Jones, Denise R.; Allamandola, Angela S.; Arthur, Jarvis J., III; Bailey, Randall E.

    2009-01-01

    By 2025, U.S. air traffic is predicted to increase three fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a revolutionary new concept has been proposed for U.S. aviation operations, termed the Next Generation Air Transportation System or "NextGen". Many key capabilities are being identified to enable NextGen, including the use of data-link communications. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen. The paper describes simulation research, conducted at National Aeronautics and Space Administration (NASA) Langley Research Center, examining data-link communications and traffic intent data during envisioned four-dimensional trajectory (4DT)-based and equivalent visual (EV) surface operations. Overall, the results suggest that controller pilot data-link communications (CPDLC) with the use of mandatory pilot read-back of all clearances significantly enhanced situation awareness for 4DT and EV surface operations. The depiction of graphical traffic state and intent information on the surface map display further enhanced off-nominal detection and pilot qualitative reports of safety and awareness.

  12. Genome Sequences of Oblitimonas alkaliphila gen. nov. sp. nov. (Proposed), a Novel Bacterium of the Pseudomonadaceae Family

    PubMed Central

    Lauer, Ana C.; Humrighouse, Ben W.; Emery, Brian; Drobish, Adam; Juieng, Phalasy; Loparev, Vladimir; McQuiston, John R.

    2015-01-01

    Results obtained through 16S rRNA gene sequencing and phenotypic testing of eight related, but unidentified, isolates located in a historical collection at the Centers for Disease Control and Prevention suggested that these isolates belong to a novel genera of bacteria. The genomes of the bacteria, to be named Oblitimonas alkaphilia gen. nov. sp. nov., were sequenced using Illumina technology. Closed genomes were produced for all eight isolates. PMID:26679585

  13. Osornodella gabrielae, n. gen. and n. sp., a new falklandellid (Amphipoda: Gammaridea) from freshwaters of the Chilean Coastal Range.

    PubMed

    Pérez-Schultheiss, Jorge

    2013-01-01

    The first species of falklandellid amphipod outside the Falkland Islands: Osornodella gabrielae n. gen., n. sp. is described from freshwaters of subterranean origin in the Coastal Range of Osorno province, Chile. The new taxon is characterized principally by the absence of secondary sexual characters in pereopods 3-4, uropod 3 aequiramous and telson slightly cleft. The new species is described and illustrated and its morphological relationships with other known species of this group are discussed. PMID:24613998

  14. Mudwigglus gen. n. (Nematoda: Diplopeltidae) from the continental slope of New Zealand, with description of three new species and notes on their distribution.

    PubMed

    Leduc, Daniel

    2013-01-01

    Three new free-living nematode species belonging to the genus Mudwigglus gen. n. are described from the continental slope of New Zealand. The new genus is characterised by four short cephalic setae, fovea amphidialis in the shape of an elongated loop, narrow mouth opening, small, lightly cuticularised buccal cavity, pharynx with oval-shaped basal bulb, and secretory-excretory pore (if present) at level of pharyngeal bulb or slightly anterior. Mudwigglus gen. et sp. n. differs from other genera of the family Diplopeltidae in the combination of the following traits: presence of reflexed ovaries, male reproductive system with both testes directed anteriorly and reflexed posterior testis, and presence of tubular pre-cloacal supplements and pre-cloacal seta. Mudwigglus patumuka gen. et sp. n. is characterised by gubernaculum with dorso-caudal apophyses, vagina directed posteriorly, and short conical tail with three terminal setae. M. macramphidum gen. et sp. n. is characterised by long fovea amphidialis, cylindrical buccal cavity, gubernaculum without apophyses, vagina at right angle to body surface, and conico-cylindrical tail without terminal setae. M. plebeius gen. et sp. n. is characterised by cylindrical buccal cavity with cuticularised ring, gubernaculum with dorso-caudal apophyses, females with vagina directed posteriorly, and conico-cylindrical tail with two terminal setae. Diplopeluta nellyae Vinex and Gourbault, 1992 is transferred to Mudwigglus gen. n. based on observations of paratypes from New Caledonia, and of specimens from the New Zealand continental slope, which both show the presence of two testes facing anteriorly. M. macramphidum gen. et sp. n. was restricted to a single site on Chatham Rise crest (350 m water depth), whereas M. patumuka gen. et sp. was recorded from six sites on western Chatham Rise (350-2800 m). M. plebeius gen. et sp. n. was recorded from 13 sites on Chatham Rise and two sites on Challenger Plateau (264-2300 m). Mudwigglus nellyae comb. n. was restricted to two Challenger Plateau sites. All Mudwigglus gen. n. species appear to be restricted to subsurface sediments. PMID:25243291

  15. Meeting Air Transportation Demand in 2025 by Using Larger Aircraft and Alternative Routing to Complement NextGen Operational Improvements

    NASA Technical Reports Server (NTRS)

    Smith, Jeremy C.; Guerreiro, Nelson M.; Viken, Jeffrey K.; Dollyhigh, Samuel M.; Fenbert, James W.

    2010-01-01

    A study was performed that investigates the use of larger aircraft and alternative routing to complement the capacity benefits expected from the Next Generation Air Transportation System (NextGen) in 2025. National Airspace System (NAS) delays for the 2025 demand projected by the Transportation Systems Analysis Models (TSAM) were assessed using NASA s Airspace Concept Evaluation System (ACES). The shift in demand from commercial airline to automobile and from one airline route to another was investigated by adding the route delays determined from the ACES simulation to the travel times used in the TSAM and re-generating new flight scenarios. The ACES simulation results from this study determined that NextGen Operational Improvements alone do not provide sufficient airport capacity to meet the projected demand for passenger air travel in 2025 without significant system delays. Using larger aircraft with more seats on high-demand routes and introducing new direct routes, where demand warrants, significantly reduces delays, complementing NextGen improvements. Another significant finding of this study is that the adaptive behavior of passengers to avoid congested airline-routes is an important factor when projecting demand for transportation systems. Passengers will choose an alternative mode of transportation or alternative airline routes to avoid congested routes, thereby reducing delays to acceptable levels for the 2025 scenario; the penalty being that alternative routes and the option to drive increases overall trip time by 0.4% and may be less convenient than the first-choice route.

  16. Mining metadata from unidentified ITS sequences in GenBank: A case study in Inocybe (Basidiomycota)

    PubMed Central

    2008-01-01

    Background The lack of reference sequences from well-identified mycorrhizal fungi often poses a challenge to the inference of taxonomic affiliation of sequences from environmental samples, and many environmental sequences are thus left unidentified. Such unidentified sequences belonging to the widely distributed ectomycorrhizal fungal genus Inocybe (Basidiomycota) were retrieved from GenBank and divided into species that were identified in a phylogenetic context using a reference dataset from an ongoing study of the genus. The sequence metadata of the unidentified Inocybe sequences stored in GenBank, as well as data from the corresponding original papers, were compiled and used to explore the ecology and distribution of the genus. In addition, the relative occurrence of Inocybe was contrasted to that of other mycorrhizal genera. Results Most species of Inocybe were found to have less than 3% intraspecific variability in the ITS2 region of the nuclear ribosomal DNA. This cut-off value was used jointly with phylogenetic analysis to delimit and identify unidentified Inocybe sequences to species level. A total of 177 unidentified Inocybe ITS sequences corresponding to 98 species were recovered, 32% of which were successfully identified to species level in this study. These sequences account for an unexpectedly large proportion of the publicly available unidentified fungal ITS sequences when compared with other mycorrhizal genera. Eight Inocybe species were reported from multiple hosts and some even from hosts forming arbutoid or orchid mycorrhizae. Furthermore, Inocybe sequences have been reported from four continents and in climate zones ranging from cold temperate to equatorial climate. Out of the 19 species found in more than one study, six were found in both Europe and North America and one was found in both Europe and Japan, indicating that at least many north temperate species have a wide distribution. Conclusion Although DNA-based species identification and circumscription are associated with practical and conceptual difficulties, they also offer new possibilities and avenues for research. Metadata assembly holds great potential to synthesize valuable information from community studies for use in a species and taxonomy-oriented framework. PMID:18282272

  17. GenSo-EWS: a novel neural-fuzzy based early warning system for predicting bank failures.

    PubMed

    Tung, W L; Quek, C; Cheng, P

    2004-05-01

    Bank failure prediction is an important issue for the regulators of the banking industries. The collapse and failure of a bank could trigger an adverse financial repercussion and generate negative impacts such as a massive bail out cost for the failing bank and loss of confidence from the investors and depositors. Very often, bank failures are due to financial distress. Hence, it is desirable to have an early warning system (EWS) that identifies potential bank failure or high-risk banks through the traits of financial distress. Various traditional statistical models have been employed to study bank failures [J Finance 1 (1975) 21; J Banking Finance 1 (1977) 249; J Banking Finance 10 (1986) 511; J Banking Finance 19 (1995) 1073]. However, these models do not have the capability to identify the characteristics of financial distress and thus function as black boxes. This paper proposes the use of a new neural fuzzy system [Foundations of neuro-fuzzy systems, 1997], namely the Generic Self-organising Fuzzy Neural Network (GenSoFNN) [IEEE Trans Neural Networks 13 (2002c) 1075] based on the compositional rule of inference (CRI) [Commun ACM 37 (1975) 77], as an alternative to predict banking failure. The CRI based GenSoFNN neural fuzzy network, henceforth denoted as GenSoFNN-CRI(S), functions as an EWS and is able to identify the inherent traits of financial distress based on financial covariates (features) derived from publicly available financial statements. The interaction between the selected features is captured in the form of highly intuitive IF-THEN fuzzy rules. Such easily comprehensible rules provide insights into the possible characteristics of financial distress and form the knowledge base for a highly desired EWS that aids bank regulation. The performance of the GenSoFNN-CRI(S) network is subsequently benchmarked against that of the Cox's proportional hazards model [J Banking Finance 10 (1986) 511; J Banking Finance 19 (1995) 1073], the multi-layered perceptron (MLP) and the modified cerebellar model articulation controller (MCMAC) [IEEE Trans Syst Man Cybern: Part B 30 (2000) 491] in predicting bank failures based on a population of 3635 US banks observed over a 21 years period. Three sets of experiments are performed-bank failure classification based on the last available financial record and prediction using financial records one and two years prior to the last available financial statements. The performance of the GenSoFNN-CRI(S) network as a bank failure classification and EWS is encouraging. PMID:15109685

  18. Melghiribacillus thermohalophilus gen. nov., sp. nov., a novel filamentous, endospore-forming, thermophilic and halophilic bacterium.

    PubMed

    Addou, Nariman Ammara; Schumann, Peter; Spröer, Cathrin; Ben Hania, Wajdi; Hacene, Hocine; Fauque, Guy; Cayol, Jean-Luc; Fardeau, Marie-Laure

    2015-04-01

    A novel filamentous, endospore-forming, thermophilic and moderately halophilic bacterium designated strain Nari2A(T) was isolated from soil collected from an Algerian salt lake, Chott Melghir. The novel isolate was Gram-staining-positive, aerobic, catalase-negative and oxidase-positive. Optimum growth occurred at 50-55 °C, 7-10% (w/v) NaCl and pH 7-8. The strain exhibited 95.4, 95.4 and 95.2% 16S rRNA gene sequence similarity to Thalassobacillus devorans G19.1(T), Sediminibacillus halophilus EN8d(T) and Virgibacillus kekensis YIM-kkny16(T), respectively. The major menaquinone was MK-7. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, three unknown phosphoglycolipids and two unknown phospholipids. The predominant cellular fatty acids were iso-C(15?:?0) and iso-C(17?:?0). The DNA G+C content was 41.9 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain Nari2A(T) is considered to represent a novel species of a new genus in the family Bacillaceae , order Bacillales , for which the name Melghiribacillus thermohalophilus gen. nov., sp. nov. is proposed. The type strain of Melghiribacillus thermohalophilus is Nari2A(T) (?=?DSM 25894(T)?=?CCUG 62543(T)). PMID:25604343

  19. Kretzoiarctos gen. nov., the Oldest Member of the Giant Panda Clade

    PubMed Central

    Abella, Juan; Alba, David M.; Robles, Josep M.; Valenciano, Alberto; Rotgers, Cheyenn; Carmona, Raül; Montoya, Plinio; Morales, Jorge

    2012-01-01

    The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8–7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12–11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint. PMID:23155439

  20. Functional Allocation for Ground-Based Automated Separation Assurance in NextGen

    NASA Technical Reports Server (NTRS)

    Prevot, Thomas; Mercer, Joey; Martin, Lynne; Homola, Jeffrey; Cabrall, Christopher; Brasil, Connie

    2010-01-01

    As part of an ongoing research effort into functional allocation in a NextGen environment, a controller-in-the-loop study on ground-based automated separation assurance was conducted at NASA Ames' Airspace Operations Laboratory in February 2010. Participants included six FAA front line managers, who are currently certified professional controllers and four recently retired controllers. Traffic scenarios were 15 and 30 minutes long where controllers interacted with advanced technologies for ground-based separation assurance, weather avoidance, and arrival metering. The automation managed the separation by resolving conflicts automatically and involved controllers only by exception, e.g., when the automated resolution would have been outside preset limits. Results from data analyses show that workload was low despite high levels of traffic, Operational Errors did occur but were closely tied to local complexity, and safety acceptability ratings varied with traffic levels. Positive feedback was elicited for the overall concept with discussion on the proper allocation of functions and trust in automation.

  1. Accelerating Our Understanding of Supernova Explosion Mechanism via Simulations and Visualizations with GenASiS

    E-print Network

    Budiardja, Reuben D; Endeve, Eirik

    2015-01-01

    Core-collapse supernovae are among the most powerful explosions in the Universe, releasing about $10^{53}~\\mbox{erg}$ of energy on timescales of a few tens of seconds. These explosion events are also responsible for the production and dissemination of most of the heavy elements, making life as we know it possible. Yet exactly how they work is still unresolved. One reason for this is the sheer complexity and cost of a self-consistent, multi-physics, and multi-dimensional core-collapse supernova simulation, which is impractical, and often impossible, even on the largest supercomputers we have available today. To advance our understanding we instead must often use simplified models, teasing out the most important ingredients for successful explosions, while helping us to interpret results from higher fidelity multi-physics models. In this paper we investigate the role of instabilities in the core-collapse supernova environment. We present here simulation and visualization results produced by our code GenASiS.

  2. Methods for Estimating Environmental Effects and Constraints on NexGen: High Density Case Study

    NASA Technical Reports Server (NTRS)

    Augustine, S.; Ermatinger, C.; Graham, M.; Thompson, T.

    2010-01-01

    This document provides a summary of the current methods developed by Metron Aviation for the estimate of environmental effects and constraints on the Next Generation Air Transportation System (NextGen). This body of work incorporates many of the key elements necessary to achieve such an estimate. Each section contains the background and motivation for the technical elements of the work, a description of the methods used, and possible next steps. The current methods described in this document were selected in an attempt to provide a good balance between accuracy and fairly rapid turn around times to best advance Joint Planning and Development Office (JPDO) System Modeling and Analysis Division (SMAD) objectives while also supporting the needs of the JPDO Environmental Working Group (EWG). In particular this document describes methods applied to support the High Density (HD) Case Study performed during the spring of 2008. A reference day (in 2006) is modeled to describe current system capabilities while the future demand is applied to multiple alternatives to analyze system performance. The major variables in the alternatives are operational/procedural capabilities for airport, terminal, and en route airspace along with projected improvements to airframe, engine and navigational equipment.

  3. GenPhilly: a strategy for improving the sustainability of aging in community initiatives.

    PubMed

    Clark, Kate

    2014-01-01

    GenPhilly is an innovative, replicable model that was developed in Philadelphia, Pennsylvania, to inspire and engage emerging leaders from a variety of disciplines to promote and sustain an aging-in-community agenda. Administrative support is provided by the Area Agency on Aging, Philadelphia Corporation for Aging, yet it was designed by its members to be peer-led. In this way, young professionals in their 20s and 30s can capitalize on popular culture to create unique professional development opportunities and get younger generations thinking about the type of city in which they themselves want to get older. The group has benefited the field of aging by building awareness of aging services in the wider community; facilitating cross-disciplinary learning and innovation around aging issues; stressing the competitive advantage for emerging leaders from all fields to know about aging issues; strengthening the aging network workforce; breaking down stereotypes about working with older adults; and introducing expertise from outside the aging network to benefit older adults. Encouraging the development of similar groups will not only benefit the field of aging, it will assist the next generation of leaders in many fields to plan better for their communities and for themselves. PMID:24266521

  4. Synthetic and Enhanced Vision Systems for NextGen (SEVS) Simulation and Flight Test Performance Evaluation

    NASA Technical Reports Server (NTRS)

    Shelton, Kevin J.; Kramer, Lynda J.; Ellis,Kyle K.; Rehfeld, Sherri A.

    2012-01-01

    The Synthetic and Enhanced Vision Systems for NextGen (SEVS) simulation and flight tests are jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA). The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SEVS operational and system-level performance capabilities. Nine test flights (38 flight hours) were conducted over the summer and fall of 2011. The evaluations were flown in Gulfstream.s G450 flight test aircraft outfitted with the SEVS technology under very low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 ft to 2400 ft visibility) into various airports from Louisiana to Maine. In-situ flight performance and subjective workload and acceptability data were collected in collaboration with ground simulation studies at LaRC.s Research Flight Deck simulator.

  5. Sapocribrum chincoteaguense n. gen. n. sp.: A Small, Scale-bearing Amoebozoan with Flabellinid Affinities.

    PubMed

    Lahr, Daniel J G; Grant, Jessica; Molestina, Robert; Katz, Laura A; Anderson, O Roger

    2015-01-01

    The isolate American Type Culture Collection (ATCC)® 50979™ is a small amoebozoan whose actin gene was previously characterized, but did not allow a stable phylogenetic placement. This isolate was originally mis-identified upon deposition, and subsequently mis-illustrated in a recent publication. Here, we provide both a detailed morphological description as well as additional molecular analyses in order to clarify the isolate's phylogenetic relationships. The amoeba is minute (less than 5 ?m), and presents the behavior of staying in a fixed location, while emitting one or two thin pseudopods. Transmission electron microscopy reveals that the cell is covered in a layer with embedded scales, giving the cell an armored appearance. Molecular phylogenetic analyses of data (actin, alpha- and beta-tubulin, elongation factor 2, and 14-3-3) from transcriptomes of this and four other isolates reveals that ATCC® 50979(™) is closely related to the recently described Squamamoeba japonica and in a novel, stable clade. Due to the unique nature of the scale covering, as well as other gross morphological characters and the molecular phylogenetic analyses, we formally describe the isolate as Sapocribrum chincoteaguense n. gen. n. sp. PMID:25515047

  6. A new tardigrade, Mutaparadoxipus duodigifinis gen. nov., sp. nov. (Heterotardigrada: Arthrotardigrada), from the Southeastern United States.

    PubMed

    Gross, Vladimir; Miller, William R; Hochberg, Rick

    2014-01-01

    A new genus and species of Arthrotardigrada is described from Florida, USA based on its unique adhesive pad/claw combinations. Mutaparadoxipus duodigifinis gen. nov., sp. nov., is characterized by well-developed, ventral secondary clavae that are adjacent to the mouth, pointed lateral and caudal alae, seminal receptacles with coiled ducts opening lateral to the gonopore, and all legs with digits bearing proximal adhesive pads. Distal claws are present on digits I-III of legs I-III, but are missing from digit IV. On leg IV, distal claws are present only on digits II & III. A single accessory point is present on claws II & III only. This is the fourth species discovered to date with proximal adhesive pads, increasing support for a clade of adhesive-padded arthrotardigrades, and is likely the sister taxon of Paradoxipus orzeliscoides. The incomplete set of claws may represent an evolutionary step in a progressive loss of claws hypothesized to have occurred within the Halechiniscidae. The subfamily Orzeliscinae is amended as a result. PMID:25081448

  7. GenInfoGuard—A Robust and Distortion-Free Watermarking Technique for Genetic Data

    PubMed Central

    Khan, Sharifullah; Anwar, Zahid; Kamran, Muhammad

    2015-01-01

    Genetic data, in digital format, is used in different biological phenomena such as DNA translation, mRNA transcription and protein synthesis. The accuracy of these biological phenomena depend on genetic codes and all subsequent processes. To computerize the biological procedures, different domain experts are provided with the authorized access of the genetic codes; as a consequence, the ownership protection of such data is inevitable. For this purpose, watermarks serve as the proof of ownership of data. While protecting data, embedded hidden messages (watermarks) influence the genetic data; therefore, the accurate execution of the relevant processes and the overall result becomes questionable. Most of the DNA based watermarking techniques modify the genetic data and are therefore vulnerable to information loss. Distortion-free techniques make sure that no modifications occur during watermarking; however, they are fragile to malicious attacks and therefore cannot be used for ownership protection (particularly, in presence of a threat model). Therefore, there is a need for a technique that must be robust and should also prevent unwanted modifications. In this spirit, a watermarking technique with aforementioned characteristics has been proposed in this paper. The proposed technique makes sure that: (i) the ownership rights are protected by means of a robust watermark; and (ii) the integrity of genetic data is preserved. The proposed technique—GenInfoGuard—ensures its robustness through the “watermark encoding” in permuted values, and exhibits high decoding accuracy against various malicious attacks. PMID:25689741

  8. Flaviaesturariibacter amylovorans gen. nov., sp. nov., a starch-hydrolysing bacterium, isolated from estuarine water.

    PubMed

    Kang, Ji Young; Chun, Jeesun; Seo, Jeong-Woo; Kim, Chul Ho; Jahng, Kwang Yeop

    2015-07-01

    A novel bacterial strain, designated GCR0105(T), was isolated from a water sample of the Mangyung estuary enclosed by the Saemangeum Embankment, located in JEOLlabuk-do, South Korea. Cells of strain GCR0105(T) were Gram-stain-negative, non-motile and rod-shaped. Colonies of strain GCR0105(T) were pale yellow-pigmented on R2A agar and nutrient agar media, and were able to grow at 15-30 °C (optimum 25 °C) and pH 6.5-8.5 (optimum pH 7.5). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GCR0105(T) was related most closely to Flavisolibacter ginsengisoli Gsoil 643(T) (93.14% similarity). The polar lipid profile of strain GCR0105(T) comprised phosphatidylethanolamine, two unknown aminolipids, an unknown aminophospholipid and four unknown lipids. The DNA G+C content of strain GCR0105(T) was 42.9 mol% and the respiratory quinone was MK-7.On the basis of phenotypic, chemotaxonomic and phylogenetic properties, strain GCR0105(T) represents a novel species in a new genus within the family Chitinophagaceae, for which the name Flaviaesturariibacter amylovorans gen. nov., sp. nov. is proposed. The type strain of Flaviaesturariibacter amylovorans is GCR0105(T) (?= KACC 16454(T) = JCM 17919(T)). PMID:25858251

  9. Flavicella marina gen. nov., sp. nov., a carotenoid-producing bacterium from surface seawater.

    PubMed

    Teramoto, Maki; Nishijima, Miyuki

    2015-03-01

    A Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped or spherical bacterium, strain 2A-7(T), was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. The strain produced a pigment(s), the absorption spectrum of which closely resembled that of ?-carotene. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Flavobacteriaceae and clustered distantly with the type strains of species of the genus Lutibacter (up to 93.9?% similarity). The DNA G+C content was 34.1 mol%. The major fatty acids were summed feature 3 (iso-C15?:?0 2-OH and/or C16?:?1?7c), iso-C17?:?0 3-OH and iso-C15?:?0 3-OH. The major polar lipids were phosphatidylethanolamine and three unidentified lipids. Menaquinone 6 was detected as the sole isoprenoid quinone. On the basis of phenotypic, genotypic and chemotaxonomic data, strain 2A-7(T) represents a novel genus and species, for which the name Flavicella marina gen. nov., sp. nov. is proposed. The type strain of Flavicella marina is 2A-7(T) (?=?NBRC 110145(T)?=?KCTC 42197(T)). PMID:25481292

  10. Molecular and morphological characterization of Veleshkinema iranicum n. gen., n. sp. (Nematoda: Hexatylina, Sphaerularioidea) from Iran.

    PubMed

    Miraeiz, Esmaeil; Heydari, Ramin; Álvarez-Ortega, Sergio; Pedram, Majid; Atighi, Mohammad Reza

    2015-01-01

    Veleshkinema  iranicum n. gen., n. sp. is described and illustrated based on morphological, morphometric and molecular characters. The new genus is characterized by having slender females and males, stylet with asymmetrical knobs, dorsal gland orifice just posterior to subventral knob, lip region with flattened apex and eight sectors, pharynx with a non-muscular and non-valvular median bulb, pharyngeal glands slightly overlapping intestine dorsally, visible cellular cardia, female with a single gonad having a quadricolumellate crustaformeria with 8-10 cells in each column, no postvulval uterine sac and rounded and offset spermatheca containing spheroid sperm cells, males with arcuate tylenchoid spicules and subterminal bursa. The new genus is morphologically compared with four genera: Abursanema, Deladenus, Prothallonema and Sphaerularia. Molecular phylogenetic studies of the new genus using 808 bp partial sequences of SSU ribosomal RNA gene placed the new genus in a clade with Sphaerularia spp. In phylogenetic analyses using 756 bp partial sequences of the 28S ribosomal RNA gene (D2-D3 segments), the new genus formed a monophyletic group with Abursanema iranicum and Sphaerularia spp. PMID:26623744

  11. Liberibacter crescens gen. nov., sp. nov., the first cultured member of the genus Liberibacter.

    PubMed

    Fagen, Jennie R; Leonard, Michael T; Coyle, Janelle F; McCullough, Connor M; Davis-Richardson, Austin G; Davis, Michael J; Triplett, Eric W

    2014-07-01

    The Gram-stain-negative, rod-shaped bacterial isolate BT-1(T) is the closest relative to the genus 'Candidatus Liberibacter' cultured to date. BT-1(T) was recovered from the phloem sap of a defoliating mountain papaya in Puerto Rico. The BT-1(T) 16S rRNA gene sequence showed that strain BT-1(T) is most closely related to members of the genus 'Ca. Liberibacter' sharing 94.7% 16S rRNA gene sequence similarity with 'Ca. Liberibacter americanus' and 'Ca. Liberibacter asiaticus'. Additionally, average nucleotide identity, 16S rRNA gene sequences and conserved protein sequences supported inclusion of the previously described species of the genus 'Ca. Liberibacter' in a genus with BT-1(T). The prominent fatty acids of isolate BT-1(T) were C18 : 1?7c (77.2%), C16 : 0 OH (4.8%), C18 : 0 (4.4%) and C16 : 0 (3.5%). Both physiological and genomic characteristics support the creation of the genus Liberibacter, as well as the novel species Liberibacter crescens gen. nov., sp. nov. with type strain BT-1(T) (?= ATCC BAA-2481(T)?= DSM 26877(T)). PMID:24786353

  12. Emergency Decay Heat Removal in a GEN-IV Gas-Cooled Fast Reactor

    SciTech Connect

    Cheng, Lap Y.; Ludewig, Hans; Jo, Jae

    2006-07-01

    A series of transient analyses using the system code RELAP5-3d has been performed to confirm the efficacy of a proposed hybrid active/passive combination approach to the decay heat removal for an advanced 2400 MWt GEN-IV gas-cooled fast reactor. The accident sequence of interest is a station blackout simultaneous with a small break (10 sq.inch/0.645 m{sup 2}) in the reactor vessel. The analyses cover the three phases of decay heat removal in a depressurization accident: (1) forced flow cooling by the power conversion unit (PCU) coast down, (2) active forced flow cooling by a battery powered blower, and (3) passive cooling by natural circulation. The blower is part of an emergency cooling system (ECS) that by design is to sustain passive decay heat removal via natural circulation cooling 24 hours after shutdown. The RELAP5 model includes the helium-cooled reactor, the ECS (primary and secondary side), the PCU with all the rotating machinery (turbine and compressors) and the heat transfer components (recuperator, pre-cooler and inter-cooler), and the guard containment that surrounds the reactor and the PCU. The transient analysis has demonstrated the effectiveness of passive decay heat removal by natural circulation cooling when the guard containment pressure is maintained at or above 800 kPa. (authors)

  13. Thermogladius shockii gen. nov., sp. nov., a hyperthermophilic crenarchaeote from Yellowstone National Park, USA.

    PubMed

    Osburn, Magdalena R; Amend, Jan P

    2011-01-01

    A hyperthermophilic heterotrophic archaeon (strain WB1) was isolated from a thermal pool in the Washburn hot spring group of Yellowstone National Park, USA. WB1 is a coccus, 0.6-1.2 ?m in diameter, with a tetragonal S-layer, vacuoles, and occasional stalk-like protrusions. Growth is optimal at 84°C (range 64-93°C), pH 5-6 (range 3.5-8.5), and <1 g/l NaCl (range 0-4.6 g/l NaCl). Tests of metabolic properties show the isolate to be a strict anaerobe that ferments complex organic substrates. Phylogenetic analysis of the 16S rRNA gene sequence places WB1 in a clade of previously uncultured Desulfurococcaceae and shows it to have ? 96% 16S rRNA sequence identity to Desulfurococcus mobilis, Staphylothermus marinus, Staphylothermus hellenicus, and Sulfophobococcus zilligii. The 16S rRNA gene contains a large insertion similar to homing endonuclease introns reported in Thermoproteus and Pyrobaculum species. Growth is unaffected by the presence of S(0) or SO(4)(2-), thereby differentiating the isolate from its closest relatives. Based on phylogenetic and physiological differences, it is proposed that isolate WB1 represents the type strain of a novel genus and species within the Desulfurococcaceae, Thermogladius shockii gen. nov., sp. nov. (RIKEN = JCM-16579, ATCC = BAA-1607, Genbank 16S rRNA gene = EU183120). PMID:20978744

  14. Haloglycomyces albus gen. nov., sp. nov., a halophilic, filamentous actinomycete of the family Glycomycetaceae.

    PubMed

    Guan, Tong-Wei; Tang, Shu-Kun; Wu, Jin-Yuan; Zhi, Xiao-Yang; Xu, Li-Hua; Zhang, Li-Li; Li, Wen-Jun

    2009-06-01

    A novel halophilic actinobacterium, designated YIM 92370(T), was isolated from a hypersaline habitat in Xinjiang Province, north-west China. The strain was aerobic, Gram-positive-staining and halophilic, with an optimum NaCl concentration for growth of 8-12 % (w/v). The whole-cell sugar pattern consisted of ribose, xylose and glucose. The predominant menaquinone was MK-9(H(4)) and the major fatty acids were iso-C(16 : 0), iso-C(17 : 0) and anteiso-C(17 : 0). The phospholipid pattern consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, two unknown phosphoglycolipids and one unknown phospholipid. The G+C content of the genomic DNA was 60.8 mol%. Phylogenetic analysis showed that strain YIM 92370(T) can be distinguished from representatives of Glycomyces and Stackebrandtia, the two existing genera in the family Glycomycetaceae, by low 16S rRNA gene sequence similarities (<93.7 %). Strain YIM 92370(T) therefore represents a novel genus and species of the family Glycomycetaceae, for which the name Haloglycomyces albus gen. nov., sp. nov. is proposed. The type strain of Haloglycomyces albus is YIM 92370(T) (=DSM 45210(T) =KCTC 19481(T)). PMID:19502305

  15. Eoetvoesia caeni gen. nov., sp. nov., isolated from an activated sludge system treating coke plant effluent.

    PubMed

    Felföldi, Tamás; Vengring, Anita; Kéki, Zsuzsa; Márialigeti, Károly; Schumann, Peter; Tóth, Erika M

    2014-06-01

    A novel bacterium, PB3-7B(T), was isolated on phenol-supplemented inorganic growth medium from a laboratory-scale wastewater purification system that treated coke plant effluent. 16S rRNA gene sequence analysis revealed that strain PB3-7B(T) belonged to the family Alcaligenaceae and showed the highest pairwise sequence similarity to Parapusillimonas granuli Ch07(T) (97.5%), Candidimonas bauzanensis BZ59(T) (97.3%) and Pusillimonas noertemannii BN9(T) (97.2%). Strain PB3-7B(T) was rod-shaped, motile and oxidase- and catalase-positive. The predominant fatty acids were C(16?:?0), C(17?:?0) cyclo, C(19?:?0) cyclo ?8c and C(14?:?0) 3-OH, and the major respiratory quinone was Q-8. The G+C content of the genomic DNA of strain PB3-7B(T) was 59.7 mol%. The novel bacterium can be distinguished from closely related type strains based on its urease activity and the capacity for assimilation of glycerol and amygdalin. On the basis of the phenotypic, chemotaxonomic and molecular data, strain PB3-7B(T) is considered to represent a new genus and species, for which the name Eoetvoesia caeni gen. nov., sp. nov. is proposed. The type strain of Eoetvoesia caeni is PB3-7B(T) (?=?DSM 25520(T)?=?NCAIM B 02512(T)). PMID:24585374

  16. Tubulideres seminoli gen. et sp. nov. and Zelinkaderes brightae sp. nov. (Kinorhyncha, Cyclorhagida) from Florida

    NASA Astrophysics Data System (ADS)

    Sørensen, Martin V.; Heiner, Iben; Ziemer, Ole; Neuhaus, Birger

    2007-12-01

    One new kinorhynch genus and species and one new species from the genus Zelinkaderes are described from sandy sediment off Fort Pierce, Florida. The new genus and species, Tubulideres seminoli gen. et sp. nov. is characterized by the presence of the first trunk segment consisting of a closed ring, the second segment of a bent tergal plate with a midventral articulation and the following nine segments consisting of a tergal and two sternal plates. Cuspidate spines are not present, but flexible tubules are located on several segments, and in particular concentrated on the ventral side of the second segment. Middorsal spines are present on all trunk segments and are alternatingly offset to a position slightly lateral to the middorsal line. Zelinkaderes brightae nov. sp. is characterized by its spine formula in having middorsal spines on trunk segments 4, 6 and 8-11, lateroventral acicular spines on segment 2, lateral accessory cuspidate spines on segments 2 and 8, ventrolateral cuspidate spines on segments 4-6 and 9, lateroventral acicular spines present on segments 8 and 9, and midterminal, lateral terminal and lateral terminal accessory spines on segment 11. The spine formula of Z. brightae nov. sp. places it in a position in between Z. submersus and a clade consisting of Z. klepali and Z. floridensis. The new findings on Z. brightae nov. sp. have led us to propose an emended diagnosis for the genus.

  17. Sulfuricella denitrificans gen. nov., sp. nov., a sulfur-oxidizing autotroph isolated from a freshwater lake.

    PubMed

    Kojima, Hisaya; Fukui, Manabu

    2010-12-01

    A novel facultatively anaerobic, sulfur-oxidizing bacterium, strain skB26(T), was isolated from anoxic water of a freshwater lake in Japan. The cells were rod-shaped, motile and Gram-negative. Strain skB26(T) oxidized elemental sulfur and thiosulfate to sulfate as sole energy sources. Strain skB26(T) was microaerobic and could also utilize nitrate as an electron acceptor, reducing it to nitrogen. Growth was observed at temperatures below 28 °C; optimum growth was observed at 22°C. The pH range for growth was 6.0-9.0, and the optimum pH was 7.5-8.0. Optimum growth of the isolate was observed in medium without NaCl, and no growth was observed in medium containing more than 220 mM NaCl. The G+C content of genomic DNA was around 59 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the strain was a member of the class Betaproteobacteria, and the closest cultivated relative was 'Thiobacillus plumbophilus' DSM 6690, with 93?% sequence similarity. Phylogenetic analyses were also performed using sequences of genes involved in sulfur oxidation, inorganic carbon fixation and nitrate respiration. On the basis of its phylogenetic and phenotypic properties, strain skB26(T) (=NBRC 105220(T) =DSM 22764(T)) is proposed as the type strain of a novel species of a new genus, Sulfuricella denitrificans gen. nov., sp. nov. PMID:20081014

  18. Using Game Theoretic Models to Predict Pilot Behavior in NextGen Merging and Landing Scenario

    NASA Technical Reports Server (NTRS)

    Yildiz, Yildiray; Lee, Ritchie; Brat, Guillaume

    2012-01-01

    In this paper, we present an implementation of the Semi Network-Form Game framework to predict pilot behavior in a merging and landing scenario. In this scenario, two aircraft are approaching to a freeze horizon with approximately equal distance when they become aware of each other via an ADS-B communication link that will be available in NextGen airspace. Both pilots want to gain advantage over the other by entering the freeze horizon earlier and obtain the first place in landing. They re-adjust their speed accordingly. However, they cannot simply increase their speed to the maximum allowable values since they are concerned with safety, separation distance, effort, possibility of being vectored-off from landing and possibility of violating speed constraints. We present how to model these concerns and the rest of the system using semi network-from game framework. Using this framework, based on certain assumptions on pilot utility functions and on system configuration, we provide estimates of pilot behavior and overall system evolution in time. We also discuss the possible employment of this modeling tool for airspace design optimization. To support this discussion, we provide a case where we investigate the effect of increasing the merging point speed limit on the commanded speed distribution and on the percentage of vectored aircraft.

  19. Tyrannobdella rex N. Gen. N. Sp. and the Evolutionary Origins of Mucosal Leech Infestations

    PubMed Central

    Phillips, Anna J.; Arauco-Brown, Renzo; Oceguera-Figueroa, Alejandro; Gomez, Gloria P.; Beltrán, María; Lai, Yi-Te; Siddall, Mark E.

    2010-01-01

    Background Leeches have gained a fearsome reputation by feeding externally on blood, often from human hosts. Orificial hirudiniasis is a condition in which a leech enters a body orifice, most often the nasopharyngeal region, but there are many cases of leeches infesting the eyes, urethra, vagina, or rectum. Several leech species particularly in Africa and Asia are well-known for their propensity to afflict humans. Because there has not previously been any data suggesting a close relationship for such geographically disparate species, this unnerving tendency to be invasive has been regarded only as a loathsome oddity and not a unifying character for a group of related organisms. Principal Findings A new genus and species of leech from Perú was found feeding from the nasopharynx of humans. Unlike any other leech previously described, this new taxon has but a single jaw with very large teeth. Phylogenetic analyses of nuclear and mitochondrial genes using parsimony and Bayesian inference demonstrate that the new species belongs among a larger, global clade of leeches, all of which feed from the mucosal surfaces of mammals. Conclusions This new species, found feeding from the upper respiratory tract of humans in Perú, clarifies an expansion of the family Praobdellidae to include the new species Tyrannobdella rex n. gen. n.sp., along with others in the genera Dinobdella, Myxobdella, Praobdella and Pintobdella. Moreover, the results clarify a single evolutionary origin of a group of leeches that specializes on mucous membranes, thus, posing a distinct threat to human health. PMID:20418947

  20. Actinorugispora endophytica gen. nov., sp. nov., an actinomycete isolated from Daucus carota.

    PubMed

    Liu, Min-Jiao; Zhu, Wen-Yong; Li, Jie; Zhao, Guo-Zhen; Xiong, Zhi; Park, Dong-Jin; Hozzein, Wael N; Kim, Chang-Jin; Li, Wen-Jun

    2015-08-01

    An actinomycete strain, designated YIM 690008T, was isolated from Daucus carota collected from South Korea and its taxonomic position was investigated by using a polyphasic approach. The strain grew well on most media tested and no diffusible pigment was produced. The aerial mycelium formed wrinkled single spores and short spore chains, some of which were branched. The whole-cell hydrolysates contained meso-diaminopimelic acid, glucose, mannose, ribose, galactose and rhamnose. The predominant menaquinones were MK-10(H4), MK-10(H6), MK-10(H8) and MK-10(H2). The polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides, some unknown phospholipids, glycolipids and polar lipids. The major fatty acids were i-C16?:?0, ai-C17?:?0 and C18?:?1?9c. The DNA G+C content of the genomic DNA was 63.1?mol%. Phylogenetic analysis indicated that the isolate belongs to the family Nocardiopsaceae. However, based on phenotypic, chemotaxonomic and genotypic data, it was concluded that strain YIM 690008T represents a novel genus and novel species of the family Nocardiopsaceae, for which the name Actinorugispora endophytica gen. nov., sp. nov. (type strain YIM 690008T?=?DSM 46770T?=?JCM 30099T?=?KCTC 29480T) is proposed. PMID:25948617

  1. Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide

    USGS Publications Warehouse

    Schaefer, J.K.; Goodwin, K.D.; McDonald, I.R.; Murrell, J.C.; Oremland, R.S.

    2002-01-01

    A marine methylotroph, designated strain MB2T, was isolated for its ability to grow on methyl bromide as a sole carbon and energy source. Methyl chloride and methyl iodide also supported growth, as did methionine and glycine betaine. A limited amount of growth was observed with dimethyl sulfide. Growth was also noted with unidentified components of the complex media marine broth 2216, yeast extract and Casamino acids. No growth was observed on methylated amines, methanol, formate, acetate, glucose or a variety of other substrates. Growth on methyl bromide and methyl iodide resulted in their oxidation to CO2 with stoichiometric release of bromide and iodide, respectively. Strain MB2T exhibited growth optima at NaCl and Mg2+ concentrations similar to that of seawater. Phylogenetic analysis of the 16S rDNA sequence placed this strain in the ??-Proteobacteria in proximity to the genera Ruegeria and Roseobacter. It is proposed that strain MB2T (= ATCC BAA-92T = DSM 14336T) be designated Leisingera methylohalidivorans gen. nov., sp. nov.

  2. Investigating contact toxicity of Geranium and Artemisia essential oils on Bemisia tabaci Gen.

    PubMed Central

    Yarahmadi, Fatemeh; Rajabpour, Ali; Zandi Sohani, Nooshin; Ramezani, Leila

    2013-01-01

    Objective: Sweet potato whitefly, Bemisia tabaci Gen. (B. tabaci), is one of the most important pests of various greenhouse crops in Iran. Nowadays, chemical insecticides are broadly used for control of the pests that causes risk to consumer's health. For the first time, contact toxicity of Pelargonium roseum Andrews and Artemisia sieberi Besser essential oils on B. tabaci and its possible application against the whitefly was evaluated in 2012. Materials and Methods: Essential oil with concentrations of 2500, 1250, 125, and 12 ppm were used. Infested leaves of greenhouse cucumber were treated by mentioned concentrations. After 24 hours, mortality of B. tabaci was recorded and compared after correcting by Abbot's formula. Results: Results showed that all concentrations of the essential oil could significantly reduce population of B. tabaci compared with the control treatment. Phytotoxicity of the treated leaves were recorded after 24, 48, and 72 hours and compared with the control. Concentrations of 2500, 1250, and 125 ppm caused severe phytotoxicity on greenhouse cucumber leaves and therefore are not suitable for greenhouse application. Phytotoxicity of 12 ppm was relatively low. Conclusions: This data implicated suitable protective effects of the essential oils to the pest infestation. Therefore, essential oils distillated from Geranium and Artemisia could be applied to control B. tabaci in greenhouse cucumber at V/V 12 ppm. PMID:25050264

  3. Bandoniozyma gen. nov., a Genus of Fermentative and Non-Fermentative Tremellaceous Yeast Species

    PubMed Central

    Landell, Melissa Fontes; Crestani, Juliana; Pagnocca, Fernando Carlos; Sette, Lara Durães; Passarini, Michel Rodrigo Zambrano; Rosa, Carlos Augusto; Brandão, Luciana R.; Pimenta, Raphael S.; Ribeiro, José Roberto; Garcia, Karina Marques; Lee, Ching-Fu; Suh, Sung-Oui; Péter, Gábor; Dlauchy, Dénes; Fell, Jack W.; Scorzetti, Gloria; Theelen, Bart; Vainstein, Marilene H.

    2012-01-01

    Background Independent surveys across the globe led to the proposal of a new basidiomycetous yeast genus within the Bulleromyces clade of the Tremellales, Bandoniozyma gen. nov., with seven new species. Methodology/Principal Findings The species were characterized by multiple methods, including the analysis of D1/D2 and ITS nucleotide sequences, and morphological and physiological/biochemical traits. Most species can ferment glucose, which is an unusual trait among basidiomycetous yeasts. Conclusions/Significance In this study we propose the new yeast genus Bandoniozyma, with seven species Bandoniozyma noutii sp. nov. (type species of genus; CBS 8364T ?=? DBVPG 4489T), Bandoniozyma aquatica sp. nov. (UFMG-DH4.20T ?=? CBS 12527T ?=? ATCC MYA-4876T), Bandoniozyma complexa sp. nov. (CBS 11570T ?=? ATCC MYA-4603T ?=? MA28aT), Bandoniozyma fermentans sp. nov. (CBS 12399T ?=? NU7M71T ?=? BCRC 23267T), Bandoniozyma glucofermentans sp. nov. (CBS 10381T ?=? NRRL Y-48076T ?=? ATCC MYA-4760T ?=? BG 02-7-15-015A-1-1T), Bandoniozyma tunnelae sp. nov. (CBS 8024T ?=? DBVPG 7000T), and Bandoniozyma visegradensis sp. nov. (CBS 12505T ?=? NRRL Y-48783T ?=? NCAIM Y.01952T). PMID:23056233

  4. Cephalothrix gen. nov. (Cyanobacteria): towards an intraspecific phylogenetic evaluation by multilocus analyses.

    PubMed

    da Silva Malone, Camila Francieli; Rigonato, Janaína; Laughinghouse, Haywood Dail; Schmidt, Éder Carlos; Bouzon, Zenilda Laurita; Wilmotte, Annick; Fiore, Marli Fátima; Sant'Anna, Célia Leite

    2015-09-01

    For more than a decade, the taxonomy of the Phormidiaceae has been problematic, since morphologically similar organisms represent phylogenetically distinct entities. Based on 16S rRNA gene sequence analyses, the polyphyletic genus Phormidium and other gas-vacuolated oscillatorioids appear scattered throughout the cyanobacterial tree of life. Recently, several studies have focused on understanding the oscillatorioid taxa at the generic level. At the specific level, few studies have characterized cyanobacterial strains using combined datasets (morphology, ultrastructure and molecular multilocus analyses). Using a multifaceted approach, we propose a new, well-defined genus, Cephalothrix gen. nov., by analysing seven filamentous strains that are morphologically 'intermediate' between gas-vacuolated taxa and Phormidium. Furthermore, we characterize two novel species: Cephalothrix komarekiana sp. nov. (strains CCIBt 3277, CCIBt 3279, CCIBt 3523, CCALA 155, SAG 75.79 and UTEX 1580) and Cephalothrix lacustris sp. nov. (strain CCIBt 3261). The generic name and specific epithets are proposed under the provisions of the International Code of Nomenclature for Algae, Fungi, and Plants. PMID:26031295

  5. Aquihabitans daechungensis gen. nov., sp. nov., an actinobacterium isolated from reservoir water.

    PubMed

    Jin, Long; Huy, Hangsak; Kim, Kwang Kyu; Lee, Hyung-Gwan; Kim, Hee-Sik; Ahn, Chi-Yong; Oh, Hee-Mock

    2013-08-01

    A novel Gram-reaction-positive bacterium, strain CH22-21(T), was isolated from a water sample taken from Daechung Reservoir, Republic of Korea, during the late-blooming period of cyanobacteria. Cells of strain CH22-21(T) were non-motile, ciliated short rods that formed creamy-white colonies on half-strength modified R2A agar. Chemotaxonomic results showed menaquinone MK-9(H6) as the predominant respiratory menaquinone, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside as major polar lipids, 16 : 1?5c, 16 : 0, 17 : 1?8c and 18 : 1?9c as major fatty acids, and a DNA G+C content of 71.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the strain formed a separate lineage within the order Acidimicrobiales, showing similarity values of <92.3 % with its closest phylogenetic neighbours. The combined genotypic and phenotypic data showed that strain CH22-21(T) could be distinguished from all genera within the order Acidimicrobiales and represented a novel species of a new genus in the family Iamiaceae, for which the name Aquihabitans dachungensis gen. nov., sp. nov. is proposed. The type strain of Aquihabitans dachungensis is CH22-21(T) (= KCTC 19849(T) = JCM 17787(T)). PMID:23378111

  6. Acetanaerobacterium elongatum gen. nov., sp. nov., from paper mill waste water.

    PubMed

    Chen, Shuangya; Dong, Xiuzhu

    2004-11-01

    Two mesophilic anaerobic bacterial strains (Z7(T) and Z1) were isolated from waste water sludge of the Xinanzhang paper mill, Beijing, China. The strains were Gram-positive, non-spore-forming and motile. Cells were thin rods (0.2-0.4x4.0-8.0 microm). Growth of the strains was observed at 20-42 degrees C and pH 5.0-7.5. Both strains hydrolysed gelatin and aesculin and fermented several kinds of mono-, di- and oligosaccharides. The fermentation end products formed from glucose were acetate, ethanol, hydrogen and carbon dioxide. The predominant cellular fatty acids were the branched-chain fatty acids isoC(15 : 0) (42.83 %) and isoC(14 : 0) (32.11 %). The DNA G+C contents of strains Z7(T) and Z1 were 50.4 and 48.6 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates represent a new phyletic sublineage within the Clostridium leptum rRNA cluster, with <91 % 16S rRNA gene sequence similarity to currently described species. On the basis of polyphasic evidence from this study, Acetanaerobacterium elongatum gen. nov., sp. nov., a novel genus and species, is proposed, with strain Z7(T) (=JCM 12359(T)=AS 1.5012(T)) as the type strain. PMID:15545467

  7. Yimella lutea gen. nov., sp. nov., a novel actinobacterium of the family Dermacoccaceae.

    PubMed

    Tang, Shu-Kun; Wu, Jin-Yuan; Wang, Yun; Schumann, Peter; Li, Wen-Jun

    2010-03-01

    A Gram-stain-positive, coccoid, non-motile, halotolerant actinobacterium, designated YIM 45900(T), was found as a contaminant on an agar plate in the laboratory of Yunnan Institute of Microbiology, China. The peptidoglycan type was A4alpha with an (L)-Lys-(L)-Ser-(D)-Asp interpeptide bridge. The cell-wall sugars contained galactose and fucose. The predominant menaquinone was MK-8(H(4)). The major fatty acids were iso-C(15 : 0), anteiso-C(15 : 0) and anteiso-C(17 : 0). The polar lipids contained diphosphatidylglycerol, phosphatidylinositol, a glucosamine-containing phospholipid and an unknown phospholipid. The DNA G+C content was 65.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism falls within the radius of the suborder Micrococcineae and its closest phylogenetic neighbours are the genera of the family Dermacoccaceae. Strain YIM 45900(T) showed 16S rRNA gene sequences similarity values of 93.1-95.9 % with members of the genera Dermacoccus, Demetria and Kytococcus. On the basis of the phylogenetic and phenotypic characteristics of the actinobacterium, a novel genus and species, Yimella lutea gen. nov., sp. nov., are proposed. The type strain of Yimella lutea is YIM 45900(T) (=DSM 19828(T) =KCTC 19231(T) =CCTCC AB 207007(T)). PMID:19656924

  8. Development of Complexity Science and Technology Tools for NextGen Airspace Research and Applications

    NASA Technical Reports Server (NTRS)

    Holmes, Bruce J.; Sawhill, Bruce K.; Herriot, James; Seehart, Ken; Zellweger, Dres; Shay, Rick

    2012-01-01

    The objective of this research by NextGen AeroSciences, LLC is twofold: 1) to deliver an initial "toolbox" of algorithms, agent-based structures, and method descriptions for introducing trajectory agency as a methodology for simulating and analyzing airspace states, including bulk properties of large numbers of heterogeneous 4D aircraft trajectories in a test airspace -- while maintaining or increasing system safety; and 2) to use these tools in a test airspace to identify possible phase transition structure to predict when an airspace will approach the limits of its capacity. These 4D trajectories continuously replan their paths in the presence of noise and uncertainty while optimizing performance measures and performing conflict detection and resolution. In this approach, trajectories are represented as extended objects endowed with pseudopotential, maintaining time and fuel-efficient paths by bending just enough to accommodate separation while remaining inside of performance envelopes. This trajectory-centric approach differs from previous aircraft-centric distributed approaches to deconfliction. The results of this project are the following: 1) we delivered a toolbox of algorithms, agent-based structures and method descriptions as pseudocode; and 2) we corroborated the existence of phase transition structure in simulation with the addition of "early warning" detected prior to "full" airspace. This research suggests that airspace "fullness" can be anticipated and remedied before the airspace becomes unsafe.

  9. Inhella inkyongensis gen. nov., sp. nov., a new freshwater bacterium in the order Burkholderiales.

    PubMed

    Song, Jaeho; Oh, Hyun-Myung; Lee, Jung-Sook; Woo, Seung-Buhm; Cho, Jang-Cheon

    2009-01-01

    A freshwater bacterium, designated IMCC1713(T), was isolated from a highly eutrophic artificial pond. Cells of the strain were Gram-negative, chemoheterotrophic, polybeat and obligately aerobic short rods that were motile with a single polar flagellum. The 16S rRNA gene sequence similarity analysis showed that the novel strain was most closely related to the species Roseateles depolymerans (96.3%), Mitsuaria chitosanitabida (96.2%), Ideonella dechloratans (96.2%), and Pelomonas saccharophila (96.1%) in the Sphaerotilus-Leptothrix group within the order Burkholderiales. Phylogenetic trees based on 16S rRNA gene sequences indicated that the isolate formed an independent monophyletic clade within the order Burkholderiales. The relatively low DNA G+C content (57.4 mol%), together with several phenotypic characteristics, differentiated the novel strain from other members of the Sphaerotilus-Leptothrix group. From the taxonomic data, therefore, the strain should be classified as a novel genus and species, for which the name Inhella inkyongensis gen. nov., sp. nov. is proposed. The type strain of the proposed species is strain IMCC1713(T) (=KCTC 12791(T)=NBRC 103252(T)=CCUG 54308(T)). PMID:19190402

  10. New data on two remarkable Antarctic species Amblydorylaimus isokaryon (Loof, 1975) Andrássy, 1998 and Pararhyssocolpus paradoxus (Loof, 1975), gen. n., comb. n. (Nematoda, Dorylaimida)

    PubMed Central

    Elshishka, Milka; Lazarova, Stela; Radoslavov, Georgi; Hristov, Petar; Peneva, Vlada K.

    2015-01-01

    Abstract The taxonomic position of two antarctic dorylaimid species Amblydorylaimus isokaryon (Loof, 1975) Andrássy, 1998 and Pararhyssocolpus paradoxus (Loof, 1975), gen. n., comb. n. are discussed on the basis of morphological, including SEM study, morphometric, postembryonic and sequence data of 18S rDNA and the D2-D3 expansion fragments of large subunit rDNA. The evolutionary trees inferred from 18S sequences show insufficient resolution to determine the assignment of the two species to particular families, moreover Pararhyssocolpus paradoxus gen. n., comb. n. (=Rhyssocolpus paradoxus) previously regarded as a member of Nordiidae or Qudsianematidae, showed distant relationship both to Rhyssocolpus vinciguerrae and Eudorylaimus spp. The phylogram inferred from 28S sequences revealed that Amblydorylaimus isokaryon is a member of a well-supported group comprised of several Aporcelaimellus spp., while, no close relationships could be revealed for the Pararhyssocolpus paradoxus gen. n., comb. n. to any nematode genus. On the basis of molecular data and morphological characteristics, some taxonomic changes are proposed. Amblydorylaimus isokaryon is transferred from family Qudsianematidae to family Aporcelaimidae, and a new monotypic genus Pararhyssocolpus gen. n. is proposed, attributed to Pararhyssocolpidae fam. n. The diagnosis of the new family is provided together with emended diagnosis of the genera Amblydorylaimus and Pararhyssocolpus gen. n. Data concerning distribution of these endemic genera in the Antarctic region are also given. PMID:26257550

  11. High quality draft genome sequence and description of Occidentia massiliensis gen. nov., sp. nov., a new member of the family Rickettsiaceae

    PubMed Central

    2014-01-01

    The family Rickettsiaceae currently includes two genera: Orientia that contains one species, Orientiatsutsugamushi, and Rickettsia that contains 28 species. Occidentia massiliensis gen. nov., sp. nov. strain OS118T is the type strain of O. massiliensis gen. nov., sp. nov., the type species of the new genus Occidentia gen. nov. within the family Rickettsiaceae. This strain, whose genome is described here, was isolated in France from the soft tick Ornithodoros sonrai collected in Senegal. O. massiliensis is an aerobic, rod-shaped, Gram-negative, obligate intracellular bacillus that may be cultivated in BME/CTVM2 cells. Here we describe the features of O. massiliensis, together with the complete genomic sequencing and annotation. The 1,469,252 bp long genome (1 chromosome but no plasmid) contains 1,670 protein-coding and 41 RNA genes, including one rRNA operon. PMID:25780502

  12. Anatoliacodium gen. nov. (Halimedaceae, Green algae) from the Ilerdian-Cuisian in the Eski?ehir region (Western Central Turkey)

    NASA Astrophysics Data System (ADS)

    Erdem, Nazire Özgen; Radoicic, Rajka

    2009-08-01

    A new genus Anatoliacodium (Halimedaceae, Green algae) is described from the Ilerdian-Cuisian shallow-water sediments of Eski?ehir region, central-western Turkey. These sequences consist of limestones, clayey limestones, sandy limestones and claystones. Anatoliacodium gen. nov. is characterized by erected calcareous segments with well differentiated inner structure: prevailing with large medulla of more or less densely set parallel filaments and cortical zone of prevailing horizontal to subhorizontal cortical filaments, once branching and without constriction. It is supposed that poorly and rarely preserved noncalcareous structures on the skeleton surface could be reproductive structures. The type species of the new genus is Anatoliacodium xinanmui gen. nov. sp. nov. A further new species is also described: Anatoliacodium merici gen. nov. sp. nov. Finally Gymnocodium nummuliticum Pfender, 1966 is emended and transferred to the genus Anatoliacodium.

  13. Genetic Epidemiology Network of Salt Sensitivity (GenSalt): Rationale, Design, Methods, and Baseline Characteristics of Study Participants

    PubMed Central

    2008-01-01

    Objective Hypertension is a complex disorder influenced by genetic and environmental determinants and their interactions. The objectives of the Genetic Epidemiology Network of Salt Sensitivity (GenSalt) are to localize and identify genes related to blood pressure (BP) responses to dietary sodium and potassium intervention. Methods GenSalt utilizes a family feeding-study design. Each family is ascertained through a proband with untreated prehypertension or stage-1 hypertension in rural China. A medical history, lifestyle risk factors, and cold pressor tests are obtained at baseline visits while BP, weight, blood and urine specimens are collected at baseline and follow-up visits. The dietary intervention includes a 7-day low sodium-feeding (51.3 mmol/day), a 7-day high sodium-feeding (307.8 mmol/day), and a 7-day high sodium-feeding with an oral potassium supplementation (60 mmol/day). Microsatellite markers for genome-wide linkage scan and SNP markers in candidate genes will be genotyped. Results Overall, 3,153 participants from 658 families were recruited for GenSalt. The mean systolic and diastolic BPs are 128.0 and 80.3, 111.6 and 71.0, 112.6 and 72.6, 106.6 and 85.3, and 136.7 and 75.0 mm Hg for probands, siblings, spouses, offspring, and parents, respectively. The mean urinary excretion of sodium and potassium are 232.5 and 38.6, 222.9 and 38.2, 213.1 and 37.8, and 207.3 and 36.0 mmol/24-hour, for probands, siblings, spouses, and offspring, respectively. Conclusions Our study will identify novel genes that interact significantly with the effect of dietary sodium and potassium intake on BP. This information is useful for development of targeted intervention for the prevention and treatment of hypertension. PMID:17443206

  14. Association of Comorbidity Burden With Abnormal Cardiac Mechanics: Findings From the HyperGEN Study

    PubMed Central

    Selvaraj, Senthil; Aguilar, Frank G.; Martinez, Eva E.; Beussink, Lauren; Kim, Kwang?Youn A.; Peng, Jie; Rasmussen?Torvik, Laura; Sha, Jin; Irvin, Marguerite R.; Gu, C. Charles; Lewis, Cora E.; Hunt, Steven C.; Arnett, Donna K.; Shah, Sanjiv J.

    2014-01-01

    Background Comorbidities are common in heart failure (HF), and the number of comorbidities has been associated with poor outcomes in HF patients. However, little is known about the effect of multiple comorbidities on cardiac mechanics, which could impact the pathogenesis of HF. We sought to determine the relationship between comorbidity burden and adverse cardiac mechanics. Methods and Results We performed speckle?tracking analysis on echocardiograms from the HyperGEN study (n=2150). Global longitudinal, circumferential, and radial strain, and early diastolic (e') tissue velocities were measured. We evaluated the association between comorbidity number and cardiac mechanics using linear mixed effects models to account for relatedness among subjects. The mean age was 51±14 years, 58% were female, and 47% were African American. Dyslipidemia and hypertension were the most common comorbidities (61% and 58%, respectively). After adjusting for left ventricular (LV) mass index, ejection fraction, and several potential confounders, the number of comorbidities remained associated with all indices of cardiac mechanics except global circumferential strain (eg, ?=?0.32 [95% CI ?0.44, ?0.20] per 1?unit increase in number of comorbidities for global longitudinal strain; ?=?0.16 [95% CI ?0.20, ?0.11] for e' velocity; P?0.0001 for both comparisons). Results were similar after excluding participants with abnormal LV geometry (P<0.05 for all comparisons). Conclusions Higher comorbidity burden is associated with worse cardiac mechanics, even in the presence of normal LV geometry. The deleterious effect of multiple comorbidities on cardiac mechanics may explain both the high comorbidity burden and adverse outcomes in patients who ultimately develop HF. PMID:24780206

  15. Description of Laccomimus gen. n. and eleven new species from the Neotropical region (Coleoptera, Dytiscidae, Laccophilinae).

    PubMed

    Toledo, Mario; Michat, Mariano C

    2015-01-01

    A new genus of laccophiline diving beetles, Laccomimus gen. n., is here described on the basis of a large number of specimens from various collections formerly misidentified as members of the Neotropical genus Laccodytes Régimbart, 1895. Except for similar size, however, the new genus is not closely related to Laccodytes. Instead, it seems to be sister to the Oriental genus Laccosternus Brancucci, 1983, both sharing a similar body size and shape, characters of the female genital structures, and shape of the prosternal process. Twelve species are recognised within Laccomimus, all new to science except Laccomimus pumilio (LeConte, 1878) comb. n., the type species. The new species are: Laccomimus alvarengi sp. n., L. amazonas sp. n., L. bolivari sp. n., L. bordoni sp. n., L. distinctus sp. n., L. improvidus sp. n., L. malkini sp. n., L. spangleri sp. n., L. spinosus sp. n., L. variegatus sp. n., L. youngi sp. n. The distribution of the new genus includes most of the Neotropics, with one species, L. pumilio, reaching Florida, USA. Each taxon is described and illustrated and a key for their identification is provided. Laccomimus is a widespread and relatively common genus in tropical America, the species of which have a wide distributional range, except for a few confined to more restricted areas. In spite of this, Laccomimus is a very uniform genus in body shape, size and colouration, and in most cases identification of the species is possible only after examination of the male genitalia. A key to distinguish genera of the tribe Laccophilini is also presented. PMID:26250237

  16. Alkalimicrobium pacificum gen. nov., sp. nov., a marine bacterium in the family Rhodobacteraceae.

    PubMed

    Zhang, Gaiyun; Yang, Yanliu; Wang, Shuang; Sun, Zhilei; Jiao, Kailin

    2015-08-01

    A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated strain F15T, was isolated from a deep-sea sediment of the western Pacific Ocean. The temperature, pH and NaCl ranges for growth were 4-50?°C, pH?6-11 and 0-10?% (w/v), respectively. Strain F15T showed the highest 16S rRNA gene sequence similarity to Sagittula stellata E-37T (96.4%), followed by Ponticoccus litoralis CL-GR66T (96.4%), Antarctobacter heliothermus EL-219T (96.3%) and Thalassococcus lentus YCS-24T (96.0%). Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain F15T formed a lineage within the family Rhodobacteraceae of the class Alphaproteobacteria. The polar lipid profile of strain F15T comprised significant amounts of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified glycolipid and one unidentified phospholipid. The predominant cellular fatty acids were summed feature 8 (C18?:?1?7c and/or C18?:?1?6c, 40.2%), anteiso-C15?:?0 (30.4%) and anteiso-C17?:?0 (9.7%). The genomic DNA G+C content of strain F15T was 60.2?mol% and the major respiratory quinone was Q-10. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain F15T is considered to represent a novel species of a new genus within the family Rhodobacteraceae, for which the name Alkalimicrobium pacificum gen. nov., sp. nov. is proposed. The type strain is F15T (?=?LMG 28107T?=?JCM 19851T?=?CGMCC 1.12763T?=?MCCC 1A09948T). PMID:25908713

  17. Pseudohalocynthiibacter aestuariivivens gen. nov., sp. nov., isolated from a tidal flat.

    PubMed

    Won, Sung-Min; Park, Sooyeon; Park, Ji-Min; Kim, Byung-Chan; Yoon, Jung-Hoon

    2015-05-01

    A Gram-stain-negative, non-motile, aerobic and coccoid, ovoid or rod-shaped bacterial strain, designated BS-W9(T), was isolated from a tidal flat of the South Sea, South Korea. Strain BS-W9(T) grew optimally at 25-30 °C, at pH 7.0-8.0 and in the presence of approximately 2.0% (w/v) NaCl. Phylogenetic trees, based on 16S rRNA gene sequences, revealed that strain BS-W9(T) clustered with the type strain of Halocynthiibacter namhaensis , showing a highest sequence similarity of 97.3%. It exhibited sequence similarity values of less than 95.6% to the type strains of other species with validly published names. Strain BS-W9(T) contained Q-10 as the predominant ubiquinone and C18:1?7c as the predominant fatty acid. The major polar lipids of strain BS-W9(T) were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The fatty acid and polar lipid profiles of strain BS-W9(T) were distinguished from those of the type strains of H. namhaensis and other phylogenetically related genera. The DNA G+C content of strain BS-W9(T) was 53.2 mol% and its mean DNA-DNA relatedness value with H. namhaensis RA2-3(T) was 14%. On the basis of the phylogenetic, chemotaxonomic and other phenotypic properties, strain BS-W9(T) is considered to represent a novel genus and species within the family Rhodobacteraceae , for which the name Pseudohalocyntiibacter aestuariivivens gen. nov., sp. nov. is proposed. The type strain of Pseudohalocyntiibacter aestuariivivens is BS-W9(T) (?=KCTC 42348(T)?=CECT 8726(T)). PMID:25713042

  18. Pharmacogenetic effects of “candidate gene complexes” on stroke in the GenHAT study

    PubMed Central

    Sørensen, Izel F.; Vazquez, Ana I.; Irvin, Marguerite R.; Sørensen, Peter; Davis, Barry R.; Ford, Charles E.; Boerwinkle, Eric; Eckfeldt, John H.; Arnett, Donna K.

    2014-01-01

    Objective The goal of this study was to investigate whether there is a genotype by treatment interaction in patients experiencing stroke and treated with one of three antihypertensive drugs, i.e. chlorthalidone, amlodipine and lisinopril. Methods A population of 436 African Americans and 539 whites that have experienced stroke in the GenHAT study were genotyped for 768 single nucleotide polymorphisms in 280 candidate genes. To detect a genotype by treatment interaction we used the Pearson's chi-square test to assess if the genotype frequencies differed at the single SNP level for the three drug treatment groups. From these single SNP analyses we derived a summary statistic for the degree of association at the gene and gene complex levels. This was done by grouping SNPs using information on gene locations and defining gene complexes based on protein-protein interactions. To assess the statistical significance of the observed test statistic we derived an empirical p-value by simulating data under the null hypothesis. Results We found that, in patients that have experienced stroke, there is a significant genetic difference between hypertension drug treatment groups. In African Americans SNP rs12143842 showed significant association (p < 0.001) with drug treatment. At gene-level HNRNPA1P4 and NOS1AP in African Americans and PRICKLE1 and NINJ2 in non-Hispanic whites were significantly associated (p < 0.01) to drug treatment, while none of the gene-complexes tested showed significance. Conclusions Based on the genetic differences between drug treatment groups, we conclude that there may be an interaction between certain genotypes and antihypertensive treatment in stroke patients. This needs to be replicated in other studies. PMID:25171760

  19. NextGen Flight Deck Surface Trajectory-Based Operations (STBO): Contingency Holds

    NASA Technical Reports Server (NTRS)

    Bakowski, Deborah Lee; Hooey, Becky Lee; Foyle, David C.; Wolter, Cynthia A.; Cheng, Lara W. S.

    2013-01-01

    The purpose of this pilot-in-the-loop taxi simulation was to investigate a NextGen Surface Trajectory-Based Operations (STBO) concept called "contingency holds." The contingency-hold concept parses a taxi route into segments, allowing an air traffic control (ATC) surface traffic management (STM) system to hold an aircraft when necessary for safety. Under nominal conditions, if the intersection or active runway crossing is clear, the hold is removed, allowing the aircraft to continue taxiing without slowing, thus improving taxi efficiency, while minimizing the excessive brake use, fuel burn, and emissions associated with stop-and-go taxi. However, when a potential traffic conflict exists, the hold remains in place as a fail-safe mechanism. In this departure operations simulation, the taxi clearance included a required time of arrival (RTA) to a specified intersection. The flight deck was equipped with speed-guidance avionics to aid the pilot in safely meeting the RTA. On two trials, the contingency hold was not released, and pilots were required to stop. On two trials the contingency hold was released 15 sec prior to the RTA, and on two trials the contingency hold was released 30 sec prior to the RTA. When the hold remained in place, all pilots complied with the hold. Results also showed that when the hold was released at 15-sec or 30-sec prior to the RTA, the 30-sec release allowed pilots to maintain nominal taxi speed, thus supporting continuous traffic flow; whereas, the 15-sec release did not. The contingency-hold concept, with at least a 30-sec release, allows pilots to improve taxiing efficiency by reducing braking, slowing, and stopping, but still maintains safety in that no pilots "busted" the clearance holds. Overall, the evidence suggests that the contingency-hold concept is a viable concept for optimizing efficiency while maintaining safety.

  20. Stackebrandtia nassauensis gen. nov., sp. nov. and emended description of the family Glycomycetaceae.

    PubMed

    Labeda, D P; Kroppenstedt, R M

    2005-07-01

    During the course of a 16S rRNA gene sequence phylogenetic evaluation of putative Glycomyces strains, it was noted that strain NRRL B-16338(T) is phylogenetically nearest to the genus Glycomyces but apparently is not a member of this or any of the other currently described actinomycete genera. The strain was subjected to a polyphasic study using standard methods for chemotaxonomic, morphological and physiological evaluation. The strain exhibited chemotaxonomic characteristics distinct from Glycomyces in spite of having 16S rRNA gene sequence similarity of 92% with the described species of this genus. The whole-cell sugar pattern of NRRL B-16338(T) consisted of ribose and inositol, with traces of arabinose and mannose. The phospholipids observed were phosphatidylglycerol and diphosphatidylglycerol and menaquinones consisting of MK-10(H(4)), MK-10(H(6)), MK-11(H(4)) and MK-11(H(6)). A significant quantity (14.5%) of 17:0 anteiso 2-hydroxy fatty acid was observed in the fatty acid profile of this strain. These characteristics clearly differentiate NRRL B-16338(T) from members of the genus Glycomyces and it is proposed that the strain represents a new genus within the family Glycomycetaceae to be called Stackebrandtia gen. nov. The description of this family is emended to permit its inclusion. It is proposed that the type species of the genus should be named Stackebrandtia nassauensis. The type strain LLR-40K-21(T) (=NRRL B-16338(T)=DSM 44728(T)) was isolated from a soil sample from Nassau, Bahamas. PMID:16014502

  1. Visual Advantage of Enhanced Flight Vision System During NextGen Flight Test Evaluation

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Harrison, Stephanie J.; Bailey, Randall E.; Shelton, Kevin J.; Ellis, Kyle K.

    2014-01-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment. Simulation and flight tests were jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA) to evaluate potential safety and operational benefits of SVS/EFVS technologies in low visibility Next Generation Air Transportation System (NextGen) operations. The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SVS/EFVS operational and system-level performance capabilities. Nine test flights were flown in Gulfstream's G450 flight test aircraft outfitted with the SVS/EFVS technologies under low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 feet to 3600 feet reported visibility) under different obscurants (mist, fog, drizzle fog, frozen fog) and sky cover (broken, overcast). Flight test videos were evaluated at three different altitudes (decision altitude, 100 feet radar altitude, and touchdown) to determine the visual advantage afforded to the pilot using the EFVS/Forward-Looking InfraRed (FLIR) imagery compared to natural vision. Results indicate the EFVS provided a visual advantage of two to three times over that of the out-the-window (OTW) view. The EFVS allowed pilots to view the runway environment, specifically runway lights, before they would be able to OTW with natural vision.

  2. Reclassification of Actinobacillus muris as Muribacter muris gen. nov., comb. nov.

    PubMed

    Nicklas, Werner; Bisgaard, Magne; Aalbæk, Bent; Kuhnert, Peter; Christensen, Henrik

    2015-10-01

    To reinvestigate the taxonomy of [Actinobacillus] muris, 474 strains, mainly from mice and rats, were characterized by phenotype and 130 strains selected for genotypic characterization by 16S rRNA and partial rpoB gene sequencing. The type strain was further investigated by whole-genome sequencing. Phylogenetic analysis of the DNA sequences showed one monophyletic group with intragroup similarities of 96.7 and 97.2?% for the 16S rRNA and rpoB genes, respectively. The highest 16S rRNA gene sequence similarity to a taxon with a validly published name outside the group was 95.9?%, to the type strain of [Pasteurella] pneumotropica. The closest related taxon based on rpoB sequence comparison was 'Haemophilus influenzae-murium', with 88.4?% similarity. A new genus and a new combination, Muribacter muris gen. nov., comb. nov., are proposed based on a distinct phylogenetic position based on 16S rRNA and rpoB gene sequence comparisons, with major divergence from the existing genera of the family Pasteurellaceae. The new genus has the characteristics of [A.] muris with the emendation that acid formation from (?-?)-d-mannitol and hydrolysis of aesculin are variable, while the ?-glucosidase test is positive. There is no requirement for exogenously supplied NAD (V factor) for the majority of strains investigated; however, one strain was found to require NAD. The major fatty acids of the type strain of Muribacter muris were C14?:?0, C14?:?0 3-OH/iso-C16?:?1 I, C16?:?1?7c and C16?:?0, which is in line with most genera of the Pasteurellaceae. The type strain of Muribacter muris is CCUG 16938T (?=?NCTC 12432T?=?ATCC 49577T). PMID:26296776

  3. Evaluation of the Gen-Probe DNA probe for the detection of legionellae in culture.

    PubMed Central

    Edelstein, P H

    1986-01-01

    A commercial DNA probe kit designed to detect rRNA from legionellae was evaluated for its ability to correctly discriminate between legionellae and non-legionellae taken from culture plates. The probe kit, made by the Gen-Probe Corp. (San Diego, Calif.), was radiolabeled with 125I, and probe bacterial RNA hybridization, detected in a simple one-tube system hybridization assay, was quantitated with a gamma counter. A total of 156 Legionella sp. strains were tested, of which 125 were Legionella pneumophila and the remainder were strains from 21 other Legionella spp. A total of 106 gram-negative non-legionellae, isolated from human respiratory tract (81%) and other body site (19%) specimens, were also tested; 14 genera and 28 species were represented. The probe easily distinguished all of the legionellae from the non-legionellae. The average legionellae/non-legionellae hybridization ratio was 42:1, and the lowest ratio was 2:1; a minor modification in the procedure increased the lowest ratio to 5:1. In addition to correctly identifying all Legionella species, the probe was able to separate some of the various species of Legionella. L. pneumophila strains hybridized more completely to the probe than did the other Legionella spp.; L. wadsworthii and L. oakridgensis hybridized only about 25% of the probe relative to L. pneumophila. Some strains of phenotypically identified L. pneumophila had much lower hybridization to the probe than other members of the species and may represent a new Legionella species. The simplicity of the technique and specificity of the probe make it a good candidate for confirming the identity of legionellae in culture. PMID:2420820

  4. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium.

    PubMed

    Derrien, Muriel; Vaughan, Elaine E; Plugge, Caroline M; de Vos, Willem M

    2004-09-01

    The diversity of mucin-degrading bacteria in the human intestine was investigated by combining culture and 16S rRNA-dependent approaches. A dominant bacterium, strain MucT, was isolated by dilution to extinction of faeces in anaerobic medium containing gastric mucin as the sole carbon and nitrogen source. A pure culture was obtained using the anaerobic soft agar technique. Strain MucT was a Gram-negative, strictly anaerobic, non-motile, non-spore-forming, oval-shaped bacterium that could grow singly and in pairs. When grown on mucin medium, cells produced a capsule and were found to aggregate. Strain MucT could grow on a limited number of sugars, including N-acetylglucosamine, N-acetylgalactosamine and glucose, but only when a protein source was provided and with a lower growth rate and final density than on mucin. The G + C content of DNA from strain MucT was 47.6 mol%. 16S rRNA gene sequence analysis revealed that the isolate was part of the division Verrucomicrobia. The closest described relative of strain MucT was Verrucomicrobium spinosum (92 % sequence similarity). Remarkably, the 16S rRNA gene sequence of strain MucT showed 99 % similarity to three uncultured colonic bacteria. According to the data obtained in this work, strain MucT represents a novel bacterium belonging to a new genus in subdivision 1 of the Verrucomicrobia; the name Akkermansia muciniphila gen. nov., sp. nov. is proposed; the type strain is MucT (= ATCC BAA-835T = CIP 107961T). PMID:15388697

  5. Chloracidobacterium thermophilum gen. nov., sp. nov.: an anoxygenic microaerophilic chlorophotoheterotrophic acidobacterium.

    PubMed

    Tank, Marcus; Bryant, Donald A

    2015-05-01

    A novel anoxygenic photoheterotrophic member of the phylum Acidobacteria , Chloracidobacterium thermophilum strain B sp. nov., was isolated from a cyanobacterial enrichment culture derived from microbial mats associated with Octopus Spring, Yellowstone National Park, WY. C. thermophilum sp. nov. was a Gram-stain-negative rod (diameter, approximately 0.8-1.0 µm; variable length, approximately 2.5 µm), which formed greenish-brown liquid suspension cultures. It was a moderately thermophilic microaerophile and grew in a defined medium at 51 °C (T(opt); range 44 to 58 °C) and in the pH range 5.5 to 9.5 (pH(opt)?=?~7.0). The DNA G+C content was 61.3 mol%, and phylogenetic analysis, based on the 16S rRNA sequence, showed that C. thermophilum sp. nov. belongs to subdivision 4 ( Acidobacteriaceae ) of the Acidobacteria . C. thermophilum sp. nov. was unable to synthesize branched-chain amino acids, L-lysine, and vitamin B12, which were required for growth. Although the organism lacked genes/enzymes for autotrophic carbon fixation, bicarbonate was required. Growth was stimulated by other amino acids and 2-oxoglutarate. Cells produced chlorosomes containing a diverse mixture of bacteriochlorophyll (BChl) c derivatives, and additionally, synthesized BChl a P, Chl a PD, and Zn-BChl a'P, which occurred in type-1 homodimeric reaction centres. The carotenoids included echinenone, canthaxanthin, lycopene, ?-carotene and ?-carotene. C. thermophilum sp. nov. produced iso-diabolic acid as its major fatty acid and synthesized three hopanoids (diploptene, bacteriohopanetetrol and bacteriohopanetetrol cyclitol ether). Based upon its phenotypic and genotypic properties, the name Chloracidobacterium thermophilum gen. nov., sp. nov. is proposed for this isolate; the type strain is C. thermophilum strain B(T) (ATCC BAA-2647 = JCM 30199). PMID:25667398

  6. Sulfurisoma sediminicola gen. nov., sp. nov., a facultative autotroph isolated from a freshwater lake.

    PubMed

    Kojima, Hisaya; Fukui, Manabu

    2014-05-01

    A novel facultatively autotrophic bacterium, strain BSN1T was isolated from sediment of a freshwater lake in Japan. The cells were rod-shaped, motile and Gram-stain-negative. As sole energy sources for autotrophic growth, the strain oxidized thiosulfate, elemental sulfur and hydrogen. Strain BSN1T was a facultative anaerobe utilizing nitrate as an electron acceptor. Growth was observed at temperatures lower than 34 °C, and the optimum growth was observed at 30-32 °C. The range of pH for growth was pH 6.8-8.8, and the optimum pH was pH 7.8-8.1. The optimum growth of the isolate occurred at concentrations of NaCl less than 50 mM. The G+C content of genomic DNA was 67 mol%. The major component in the fatty acid profile of strain BSN1T grown on fumarate was summed feature 3 (C16:1?7c and/or iso-C15:0 2-OH). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was a member of the class Betaproteobacteria, and it showed the highest sequence similarity with Georgfuchsia toluolica G5G6T (96.2%). Phylogenetic analyses were also performed on genes involved in sulfur oxidation. On the basis of its phylogenetic and phenotypic properties, strain BSN1T (=DSM 26916T=NBRC 109412T) is proposed as the type strain of a novel species of a novel genus, Sulfurisoma sediminicola gen. nov., sp. nov. PMID:24480906

  7. Sulfuritalea hydrogenivorans gen. nov., sp. nov., a facultative autotroph isolated from a freshwater lake.

    PubMed

    Kojima, Hisaya; Fukui, Manabu

    2011-07-01

    A novel facultatively autotrophic bacterium, designated strain sk43H(T), was isolated from water of a freshwater lake in Japan. Cells of the isolate were curved rods, motile and gram-reaction-negative. Strain sk43H(T) was facultatively anaerobic and autotrophic growth was observed only under anaerobic conditions. The isolate oxidized thiosulfate, elemental sulfur and hydrogen as sole energy sources for autotrophic growth and could utilize nitrate as an electron acceptor. Growth was observed at 8-32 °C (optimum 25 °C) and 6.4-7.6 (optimum pH 6.7-6.9). Optimum growth of the isolate occurred at NaCl concentrations of less than 50 mM. The G+C content of genomic DNA was around 67 mol%. The fatty acid profile of strain sk43H(T) when grown on acetate under aerobic conditions was characterized by the presence of C(16?:?0) and summed feature 3 (C(16?:?1)?7c and/or iso-C(15?:?0) 2-OH) as the major components. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was a member of the class Betaproteobacteria showing highest sequence similarity with Georgfuchsia toluolica G5G6(T) (94.7?%) and Denitratisoma oestradiolicum AcBE2-1(T) (94.3?%). Phylogenetic analyses were also performed using genes involved in sulfur oxidation. On the basis of its phylogenetic and phenotypic properties, strain sk43H(T) (?=?DSM 22779(T) ?=?NBRC 105852(T)) represents a novel species of a new genus, for which the name Sulfuritalea hydrogenivorans gen. nov., sp. nov. is proposed. PMID:20709913

  8. Aliisedimentitalea scapharcae gen. nov., sp. nov., isolated from ark shell Scapharca broughtonii.

    PubMed

    Kim, Young-Ok; Park, Sooyeon; Nam, Bo-Hye; Kim, Dong-Gyun; Won, Sung-Min; Park, Ji-Min; Yoon, Jung-Hoon

    2015-08-01

    A Gram-negative, aerobic, non-spore-forming, motile and ovoid or rod-shaped bacterial strain, designated MA2-16(T), was isolated from ark shell (Scapharca broughtonii) collected from the South Sea, South Korea. Strain MA2-16(T) was found to grow optimally at 30°C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain MA2-16(T) clustered with the type strain of Sedimentitalea nanhaiensis. The novel strain exhibited a 16S rRNA gene sequence similarity value of 97.1% to the type strain of S. nanhaiensis. In the neighbour-joining phylogenetic tree based on gyrB sequences, strain MA2-16(T) formed an evolutionary lineage independent of those of other taxa. Strain MA2-16(T) contained Q-10 as the predominant ubiquinone and C18:1 ?7c and 11-methyl C18:1 ?7c as the major fatty acids. The major polar lipids of strain MA2-16(T) were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of strain MA2-16(T) was 57.7 mol% and its DNA-DNA relatedness values with the type strains of S. nanhaiensis and some phylogenetically related species of the genera Leisingera and Phaeobacter were 13-24%. On the basis of the data presented, strain MA2-16(T) is considered to represent a novel genus and novel species within the family Rhodobacteraceae, for which the name Aliisedimentitalea scapharcae gen. nov., sp. nov. is proposed. The type strain is MA2-16(T) (=KCTC 42119(T) =CECT 8598(T)). PMID:26224451

  9. Feasibility of a Networked Air Traffic Infrastructure Validation Environment for Advanced NextGen Concepts

    NASA Technical Reports Server (NTRS)

    McCormack, Michael J.; Gibson, Alec K.; Dennis, Noah E.; Underwood, Matthew C.; Miller,Lana B.; Ballin, Mark G.

    2013-01-01

    Abstract-Next Generation Air Transportation System (NextGen) applications reliant upon aircraft data links such as Automatic Dependent Surveillance-Broadcast (ADS-B) offer a sweeping modernization of the National Airspace System (NAS), but the aviation stakeholder community has not yet established a positive business case for equipage and message content standards remain in flux. It is necessary to transition promising Air Traffic Management (ATM) Concepts of Operations (ConOps) from simulation environments to full-scale flight tests in order to validate user benefits and solidify message standards. However, flight tests are prohibitively expensive and message standards for Commercial-off-the-Shelf (COTS) systems cannot support many advanced ConOps. It is therefore proposed to simulate future aircraft surveillance and communications equipage and employ an existing commercial data link to exchange data during dedicated flight tests. This capability, referred to as the Networked Air Traffic Infrastructure Validation Environment (NATIVE), would emulate aircraft data links such as ADS-B using in-flight Internet and easily-installed test equipment. By utilizing low-cost equipment that is easy to install and certify for testing, advanced ATM ConOps can be validated, message content standards can be solidified, and new standards can be established through full-scale flight trials without necessary or expensive equipage or extensive flight test preparation. This paper presents results of a feasibility study of the NATIVE concept. To determine requirements, six NATIVE design configurations were developed for two NASA ConOps that rely on ADS-B. The performance characteristics of three existing in-flight Internet services were investigated to determine whether performance is adequate to support the concept. Next, a study of requisite hardware and software was conducted to examine whether and how the NATIVE concept might be realized. Finally, to determine a business case, economic factors were evaluated and a preliminary cost-benefit analysis was performed.

  10. Visual advantage of enhanced flight vision system during NextGen flight test evaluation

    NASA Astrophysics Data System (ADS)

    Kramer, Lynda J.; Harrison, Stephanie J.; Bailey, Randall E.; Shelton, Kevin J.; Ellis, Kyle K. E.

    2014-06-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment. Simulation and flight tests were jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA) to evaluate potential safety and operational benefits of SVS/EFVS technologies in low visibility Next Generation Air Transportation System (NextGen) operations. The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SVS/EFVS operational and system-level performance capabilities. Nine test flights were flown in Gulfstream's G450 flight test aircraft outfitted with the SVS/EFVS technologies under low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 feet to 3600 feet reported visibility) under different obscurants (mist, fog, drizzle fog, frozen fog) and sky cover (broken, overcast). Flight test videos were evaluated at three different altitudes (decision altitude, 100 feet radar altitude, and touchdown) to determine the visual advantage afforded to the pilot using the EFVS/Forward-Looking InfraRed (FLIR) imagery compared to natural vision. Results indicate the EFVS provided a visual advantage of two to three times over that of the out-the-window (OTW) view. The EFVS allowed pilots to view the runway environment, specifically runway lights, before they would be able to OTW with natural vision.

  11. Thalassolituus oleivorans gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons.

    PubMed

    Yakimov, Michail M; Giuliano, Laura; Denaro, Renata; Crisafi, Ermanno; Chernikova, Tatiana N; Abraham, Wolf-Rainer; Luensdorf, Heinrich; Timmis, Kenneth N; Golyshin, Peter N

    2004-01-01

    An aerobic, heterotrophic, Gram-negative, curved bacterial strain, designated MIL-1T, was isolated by extinction dilution from an n-tetradecane enrichment culture that was established from sea water/sediment samples collected in the harbour of Milazzo, Italy. In the primary enrichment, the isolate formed creamy-white, medium-sized colonies on the surface of the agar. The isolate did not grow in the absence of NaCl; growth was optimal at 2.7% NaCl. Only a narrow spectrum of organic compounds, including aliphatic hydrocarbons (C7-C20), their oxidized derivatives and acetate, were used as growth substrates. The isolate was not able to grow under denitrifying conditions. The DNA G+C content and genome size of strain MIL-1T were estimated to be 53.2 mol% and 2.2 Mbp, respectively. The major cellular and phospholipid fatty acids were palmitoleic, palmitic and oleic acids (33.5, 29.5 and 11.0% and 18, 32 and 31%, respectively). 3-hydroxy lauric acid was the only hydroxy fatty acid detected. Thirteen different compounds that belonged to two types of phospholipid (phosphatidylethylamine and phosphatidylglycerol) were identified. 16S rRNA gene sequence analysis revealed that this isolate represents a distinct phyletic lineage within the gamma-Proteobacteria and has about 94.4% sequence similarity to Oceanobacter kriegii (the closest bacterial species with a validly published name). The deduced protein sequence of the putative alkane hydrolase, AlkB, of strain MIL-1T is related to the corresponding enzymes of Alcanivorax borkumensis and Pseudomonas oleovorans (81 and 80% similarity, respectively). On the basis of the analyses performed, Thalassolituus oleivorans gen. nov., sp. nov. is described. Strain MIL-1T (=DSM 14913T=LMG 21420T) is the type and only strain of T. oleivorans. PMID:14742471

  12. Mumia flava gen. nov., sp. nov., an actinobacterium of the family Nocardioidaceae.

    PubMed

    Lee, Learn-Han; Zainal, Nurullhudda; Azman, Adzzie-Shazleen; Mutalib, Nurul-Syakima Ab; Hong, Kui; Chan, Kok-Gan

    2014-05-01

    A novel actinobacterial strain, designated MUSC 201T, was isolated from a mangrove soil collected from Kuantan, the capital city of Pahang State in Malaysia. The taxonomic status of this strain was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis revealed that strain MUSC 201T represented a novel lineage within the class Actinobacteria. Strain MUSC 201T formed a distinct clade in the family Nocardioidaceae and was most closely related to the members of the genera Nocardioides (16S rRNA gene sequence similarity, 91.9-95.1%), Aeromicrobium (92.7-94.6%), Marmoricola (92.5-93.1%) and Kribbella (91.5-92.4%). The cells of this strain were irregular coccoid to short rod shaped. The peptidoglycan contained ll-diaminopimelic acid as diagnostic diamino acid and the peptidoglycan type was A3?. The peptidoglycan cell wall contained ll-diaminopimelic acid, glycine, glutamic acid and alanine in a molar ratio of 1.5:0.9:1.0:1.5. The cell-wall sugars were galactose and rhamnose. The predominant menaquinone was MK-9(H4). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, glycolipid and four unknown phospholipids. The major cellular fatty acids were C18:1?9c (30.8%), C16:0 (24.1%), and 10-methyl C18:0 (13.9%). The DNA G+C content was 72.0±0.1 mol%. On the basis of phylogenetic and phenotypic differences from members of the genera of the family Nocardioidaceae, a novel genus and species, Mumia flava gen. nov., sp. nov. are proposed. The type strain of Mumia flava is MUSC 201T (=DSM 27763T=MCCC 1A00646T=NBRC 109973T). PMID:24449791

  13. Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis

    NASA Technical Reports Server (NTRS)

    Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Matsa, M. E.; Peng, C. K.; Simons, M.; Stanley, H. E.

    1995-01-01

    An open question in computational molecular biology is whether long-range correlations are present in both coding and noncoding DNA or only in the latter. To answer this question, we consider all 33301 coding and all 29453 noncoding eukaryotic sequences--each of length larger than 512 base pairs (bp)--in the present release of the GenBank to dtermine whether there is any statistically significant distinction in their long-range correlation properties. Standard fast Fourier transform (FFT) analysis indicates that coding sequences have practically no correlations in the range from 10 bp to 100 bp (spectral exponent beta=0.00 +/- 0.04, where the uncertainty is two standard deviations). In contrast, for noncoding sequences, the average value of the spectral exponent beta is positive (0.16 +/- 0.05) which unambiguously shows the presence of long-range correlations. We also separately analyze the 874 coding and the 1157 noncoding sequences that have more than 4096 bp and find a larger region of power-law behavior. We calculate the probability that these two data sets (coding and noncoding) were drawn from the same distribution and we find that it is less than 10(-10). We obtain independent confirmation of these findings using the method of detrended fluctuation analysis (DFA), which is designed to treat sequences with statistical heterogeneity, such as DNA's known mosaic structure ("patchiness") arising from the nonstationarity of nucleotide concentration. The near-perfect agreement between the two independent analysis methods, FFT and DFA, increases the confidence in the reliability of our conclusion.

  14. Luteipulveratus mongoliensis gen. nov., sp. nov., an actinobacterial taxon in the family Dermacoccaceae.

    PubMed

    Ara, Ismet; Yamamura, Hideki; Tsetseg, Baljinova; Daram, Damdinsuren; Ando, Katsuhiko

    2010-03-01

    A novel actinobacterial strain, MN07-A0370(T), was isolated from Mongolian soil and its taxonomic status was determined using a polyphasic approach. Comparative 16S rRNA gene sequence studies revealed that strain MN07-A0370(T) represented a novel lineage within the actinobacteria. Strain MN07-A0370(T) formed a distinct clade in the family Dermacoccaceae and was most closely related to the members of the genera Dermacoccus (16S rRNA gene sequence similarity, 96.2 %-96.4 %), Demetria (94.1 %) and Kytococcus (93.7 %). The cell-wall peptidoglycan of the novel strain contained l-lysine, alanine, aspartic acid, glutamic acid and serine and represented peptidoglycan type A4alpha. The menaquinones were MK-8(H(4)) and MK-8(H(6)). The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol and the whole-cell sugars were galactose, mannose, rhamnose, ribose and glucose. Mycolic acids were absent. The fatty acid profile was characterized by the presence of large amounts of saturated iso- and anteiso-branched-chain fatty acids as well as smaller amounts of saturated straight-chain and unsaturated acids. The major fatty acids were iso-C(16 : 0), anteiso-C(17 : 0), iso-C(16 : 1) H, C(17 : 1)omega9c and C(17 : 0) 10-methyl. The G+C content of the DNA was 68.2 mol%. On the basis of chemotaxonomic, physiological and biochemical differences from other genera of the family Dermacoccaceae, strain MN07-A0370(T) should be classified as representing a novel species in a new genus, for which we propose the name Luteipulveratus mongoliensis gen. nov., sp. nov. The type strain is MN07-A0370(T) (=NBRC 105296(T)=VTCC D9-09(T)). PMID:19654344

  15. Barrientosiimonas humi gen. nov., sp. nov., an actinobacterium of the family Dermacoccaceae.

    PubMed

    Lee, Learn-Han; Cheah, Yoke-Kqueen; Sidik, Shiran Mohd; Xie, Qing-Yi; Tang, Yi-Li; Lin, Hai-Peng; Mutalib, Nurul-Syakima Ab; Hong, Kui

    2013-01-01

    Three novel actinobacteria, strains 39(T), 40 and 41, were isolated from soil collected from Barrientos Island in the Antarctic. The taxonomic status of these strains was determined using a polyphasic approach. Comparison of 16S rRNA gene sequences revealed that strain 39(T) represented a novel lineage within the family Dermacoccaceae and was most closely related to members of the genera Demetria (96.9 % 16S rRNA gene sequence similarity), Branchiibius (95.7 %), Dermacoccus (94.4-95.3 %), Calidifontibacter (94.6 %), Luteipulveratus (94.3 %), Yimella (94.2 %) and Kytococcus (93.1 %). Cells were irregular cocci and short rods. The peptidoglycan type was A4? with an L-Lys-L-Ser-D-Asp interpeptide bridge. The cell-wall sugars were galactose and glucose. The major menaquinone was MK-8(H(4)). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphoglycolipid, two glycolipids and one unknown phospholipid. The acyl type of the cell-wall polysaccharide was N-acetyl. The major cellular fatty acids were anteiso-C(17 : 0) (41.97 %), anteiso-C(17 : 1)?9c (32.16 %) and iso-C(16 : 0) (7.68 %). The DNA G+C content of strain 39(T) was 68.4 mol%. On the basis of phylogenetic and phenotypic differences from other genera of the family Dermacoccaceae, a novel genus and species, Barrientosiimonas humi gen. nov., sp. nov., is proposed; the type strain of the type species is 39(T) (=CGMCC 4.6864(T) = DSM 24617(T)). PMID:22389286

  16. Algoriella xinjiangensis gen. nov., sp. nov., a new psychrotolerant bacterium of the family Flavobacteriaceae.

    PubMed

    Yang, Na; Zhang, Lixin; Sun, Chaomin

    2015-11-01

    An aerobic, Gram-stain negative, non-spore-forming and psychrotolerant bacterium, designated strain XJ109(T), was isolated from a sewage water sample collected from Xinjiang Uigur Autonomous Region, China. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain XJ109(T) represents a novel member of the family Flavobacteriaceae. The strain showed 95.5 % similarity with the 16S rRNA gene sequence of Empedobacter brevis LMG 4011(T), 95.4 % with Chishuiella changwenlii BY4(T), 95.3 % with Empedobacter falsenii NF 993(T) and 92.3 % with Weeksella virosa DSM 16922(T). Strain XJ109(T) showed the common phenotypic and chemotaxonomic characteristics of the family Flavobacteriaceae, containing menaquinone-6 (MK-6) as the predominant respiratory quinone and iso-C17:0 3OH and iso-C15:0 as the major fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, one unidentified phospholipid and two unidentified lipids. The genomic DNA G+C content was 38.0 mol%. Strain XJ109(T) was positive for catalase and oxidase activities, and it was observed to grow at 4-30 °C (optimal 16-20 °C), pH 6.5-10.0 (optimal 7.0-7.5) and in media containing 0-2.0 % (w/v) NaCl (optimal 0.5 %). On the basis of the polyphasic evidence presented, strain XJ109(T) is considered to represent a novel genus and species of the family Flavobacteriaceae, for which the name Algoriella xinjiangensis gen. nov., sp. nov. is proposed. The type strain is XJ109(T) (=CGMCC 1.10229(T)=JCM 16590(T)). PMID:26310805

  17. Modeling and Evaluating Pilot Performance in NextGen: Review of and Recommendations Regarding Pilot Modeling Efforts, Architectures, and Validation Studies

    NASA Technical Reports Server (NTRS)

    Wickens, Christopher; Sebok, Angelia; Keller, John; Peters, Steve; Small, Ronald; Hutchins, Shaun; Algarin, Liana; Gore, Brian Francis; Hooey, Becky Lee; Foyle, David C.

    2013-01-01

    NextGen operations are associated with a variety of changes to the national airspace system (NAS) including changes to the allocation of roles and responsibilities among operators and automation, the use of new technologies and automation, additional information presented on the flight deck, and the entire concept of operations (ConOps). In the transition to NextGen airspace, aviation and air operations designers need to consider the implications of design or system changes on human performance and the potential for error. To ensure continued safety of the NAS, it will be necessary for researchers to evaluate design concepts and potential NextGen scenarios well before implementation. One approach for such evaluations is through human performance modeling. Human performance models (HPMs) provide effective tools for predicting and evaluating operator performance in systems. HPMs offer significant advantages over empirical, human-in-the-loop testing in that (1) they allow detailed analyses of systems that have not yet been built, (2) they offer great flexibility for extensive data collection, (3) they do not require experimental participants, and thus can offer cost and time savings. HPMs differ in their ability to predict performance and safety with NextGen procedures, equipment and ConOps. Models also vary in terms of how they approach human performance (e.g., some focus on cognitive processing, others focus on discrete tasks performed by a human, while others consider perceptual processes), and in terms of their associated validation efforts. The objectives of this research effort were to support the Federal Aviation Administration (FAA) in identifying HPMs that are appropriate for predicting pilot performance in NextGen operations, to provide guidance on how to evaluate the quality of different models, and to identify gaps in pilot performance modeling research, that could guide future research opportunities. This research effort is intended to help the FAA evaluate pilot modeling efforts and select the appropriate tools for future modeling efforts to predict pilot performance in NextGen operations.

  18. Accuracy evaluation of ClimGen weather generator and daily to hourly disaggregation methods in tropical conditions

    NASA Astrophysics Data System (ADS)

    Safeeq, Mohammad; Fares, Ali

    2011-12-01

    Daily and sub-daily weather data are often required for hydrological and environmental modeling. Various weather generator programs have been used to generate synthetic climate data where observed climate data are limited. In this study, a weather data generator, ClimGen, was evaluated for generating information on daily precipitation, temperature, and wind speed at four tropical watersheds located in Hawai`i, USA. We also evaluated different daily to sub-daily weather data disaggregation methods for precipitation, air temperature, dew point temperature, and wind speed at M?kaha watershed. The hydrologic significance values of the different disaggregation methods were evaluated using Distributed Hydrology Soil Vegetation Model. MuDRain and diurnal method performed well over uniform distribution in disaggregating daily precipitation. However, the diurnal method is more consistent if accurate estimates of hourly precipitation intensities are desired. All of the air temperature disaggregation methods performed reasonably well, but goodness-of-fit statistics were slightly better for sine curve model with 2 h lag. Cosine model performed better than random model in disaggregating daily wind speed. The largest differences in annual water balance were related to wind speed followed by precipitation and dew point temperature. Simulated hourly streamflow, evapotranspiration, and groundwater recharge were less sensitive to the method of disaggregating daily air temperature. ClimGen performed well in generating the minimum and maximum temperature and wind speed. However, for precipitation, it clearly underestimated the number of extreme rainfall events with an intensity of >100 mm/day in all four locations. ClimGen was unable to replicate the distribution of observed precipitation at three locations (Honolulu, Kahului, and Hilo). ClimGen was able to reproduce the distributions of observed minimum temperature at Kahului and wind speed at Kahului and Hilo. Although the weather data generation and disaggregation methods were concentrated in a few Hawaiian watersheds, the results presented can be used to similar mountainous location settings, as well as any specific locations aimed at furthering the site-specific performance evaluation of these tested models.

  19. Phylogenetic relationships among species of Williopsis and Saturnospora gen. nov. as determined from partial rRNA sequences.

    PubMed

    Liu, Z W; Kurtzman, C P

    1991-07-01

    Phylogenetic relationships among those yeast species that form saturn-shaped ascospores and which are assigned to the genera Williopsis and Pichia were estimated from their extent of nucleotide sequence divergence in three regions of ribosomal RNA. The Pichia species (P. dispora, P. saitoi, P. zaruensis and P. sp. nov.) are a closely clustered group only distantly related to Williopsis, and it is proposed that they be reassigned to Saturnospora gen. nov. The extent of divergence among Williopsis species (W. californica, W. mucosa, W. pratensis, W. saturnus and W. sp. nov.) is greater than that previously observed within other ascomycetous yeast genera. PMID:1796804

  20. A new member of troglobitic Carychiidae, Koreozospeum nodongense gen. et sp. n. (Gastropoda, Eupulmonata, Ellobioidea) is described from Korea.

    PubMed

    Jochum, Adrienne; Prozorova, Larisa; Sharyi-Ool, Mariana; Páll-Gergely, Barna

    2015-01-01

    A new genus of troglobitic Carychiidae Jeffreys, 1830 is designated from Nodong Cave, North Chungcheong Province, Danyang, South Korea. This remarkable find represents a great range extension and thus, a highly distant distribution of troglobitic Carychiidae in Asia. The Zospeum-like, carychiid snails were recently included, without a formal description, in records documenting Korean malacofauna. The present paper describes Koreozospeum Jochum & Prozorova, gen. n. and illustrates the type species, Koreozospeum nodongense Lee, Prozorova & Jochum, sp. n. using novel Nano-CT images, including a video, internal shell morphology, SEM and SEM-EDX elemental compositional analysis of the shell. PMID:26312456

  1. A new member of troglobitic Carychiidae, Koreozospeum nodongense gen. et sp. n. (Gastropoda, Eupulmonata, Ellobioidea) is described from Korea

    PubMed Central

    Jochum, Adrienne; Prozorova, Larisa; Sharyi-ool, Mariana; Páll-Gergely, Barna

    2015-01-01

    Abstract A new genus of troglobitic Carychiidae Jeffreys, 1830 is designated from Nodong Cave, North Chungcheong Province, Danyang, South Korea. This remarkable find represents a great range extension and thus, a highly distant distribution of troglobitic Carychiidae in Asia. The Zospeum-like, carychiid snails were recently included, without a formal description, in records documenting Korean malacofauna. The present paper describes Koreozospeum Jochum & Prozorova, gen. n. and illustrates the type species, Koreozospeum nodongense Lee, Prozorova & Jochum, sp. n. using novel Nano-CT images, including a video, internal shell morphology, SEM and SEM-EDX elemental compositional analysis of the shell. PMID:26312456

  2. search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information

    PubMed Central

    2013-01-01

    Background Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. Results We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user’s query, advanced data searching based on the specified user’s query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. Conclusions search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/. PMID:23452691

  3. A new genus and species of isanthid sea anemone (Cnidaria: Anthozoa: Actiniaria) from Chilean Patagonia, Anthoparactis fossii n. gen. et sp

    NASA Astrophysics Data System (ADS)

    Häussermann, Verena; Rodríguez, Estefanía

    2014-09-01

    We describe a new genus and species of sea anemone from Chilean Patagonia. Anthoparactis fossii n. gen. et sp. adds another acontiate genus and species to the family Isanthidae Carlgren, 1938. Anthoparactis n. gen. differs from the other isanthid genera in having the same number of mesenteries distally and proximally, acontia with basitrichs only, and a column with verrucae distally. Anthoparactis fossii n. sp. differs from the most similar species, Isoparactis fionae Lauretta et al., 2013, in the number of cycles of mesenteries and tentacles, structures of the column, colour pattern of the oral disc, cnidae, and geographical distribution. Isanthidae now includes seven genera and 11 species.

  4. Comparative Evaluation of Two PCR-Based Methods for Detection of Methicillin-Resistant Staphylococcus aureus (MRSA): Xpert MRSA Gen 3 and BD-Max MRSA XT.

    PubMed

    Lepainteur, Margaux; Delattre, Sandrine; Cozza, Sophie; Lawrence, Christine; Roux, Anne-Laure; Rottman, Martin

    2015-06-01

    We compared two walk-away molecular diagnostic assays, the GeneXpert MRSA Gen 3 assay and the BD-Max MRSA XT assay. A total of 119 prospective swabs and 36 culture-positive samples were tested. Xpert MRSA Gen 3 had sensitivity of 95.7% and specificity of 100% versus 87.5% and 97.1% for BD-Max. The difference in agreement with the enriched culture results was significantly in favor of the Xpert assay (P < 0.02, McNemar nonparametric text). PMID:25878336

  5. Herbinix hemicellulosilytica gen. nov., sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor.

    PubMed

    Koeck, Daniela E; Ludwig, Wolfgang; Wanner, Gerhard; Zverlov, Vladimir V; Liebl, Wolfgang; Schwarz, Wolfgang H

    2015-08-01

    Phenotypic and phylogenetic studies were performed on new isolates of a novel Gram-stain-positive, anaerobic, non-sporulating, rod-shaped bacterium isolated from a thermophilic biogas plant. The novel organisms were able to degrade crystalline cellulose. 16S rRNA gene comparative sequence analysis demonstrated that the isolates formed a hitherto unknown subline within the family Lachnospiraceae. As a representative of the whole group of isolates, strain T3/55T was further characterized. The closest relative of T3/55T among the taxa with validly published names is Mobilitalea sibirica, sharing 93.9% 16S rRNA gene sequence similarity. Strain T3/55T was catalase-negative, indole-negative, and produced acetate, ethanol and propionic acid as major end products from cellulose metabolism. The major cellular fatty acids (>1%) were 16?:?0 dimethyl acetal, 16?:?0 fatty acid methyl ester and 16?:?0 aldehyde. The DNA G+C content was 36.6?mol%. A novel genus and species, Herbinix hemicellulosilytica gen. nov., sp. nov., is proposed based on phylogenetic analysis and physiological properties of the novel isolate. Strain T3/55T (?=?DSM 29228T?=?CECT 8801T), represents the type strain of Herbinix hemicellulosilytica gen. nov., sp. nov. PMID:25872956

  6. Phylotranscriptomics: Saturated Third Codon Positions Radically Influence the Estimation of Trees Based on Next-Gen Data

    PubMed Central

    Breinholt, Jesse W.; Kawahara, Akito Y.

    2013-01-01

    Recent advancements in molecular sequencing techniques have led to a surge in the number of phylogenetic studies that incorporate large amounts of genetic data. We test the assumption that analyzing large number of genes will lead to improvements in tree resolution and branch support using moths in the superfamily Bombycoidea, a group with some interfamilial relationships that have been difficult to resolve. Specifically, we use a next-gen data set that included 19 taxa and 938 genes (?1.2M bp) to examine how codon position and saturation might influence resolution and node support among three key families. Maximum likelihood, parsimony, and species tree analysis using gene tree parsimony, on different nucleotide and amino acid data sets, resulted in largely congruent topologies with high bootstrap support compared with prior studies that included fewer loci. However, for a few shallow nodes, nucleotide and amino acid data provided high support for conflicting relationships. The third codon position was saturated and phylogenetic analysis of this position alone supported a completely different, potentially misleading sister group relationship. We used the program RADICAL to assess the number of genes needed to fix some of these difficult nodes. One such node originally needed a total of 850 genes but only required 250 when synonymous signal was removed. Our study shows that, in order to effectively use next-gen data to correctly resolve difficult phylogenetic relationships, it is necessary to assess the effects of synonymous substitutions and third codon positions. PMID:24148944

  7. New Australian stiletto flies: revision of Manestella Metz and description of Medomega gen. n. (Diptera, Therevidae, Agapophytinae)

    PubMed Central

    Winterton, Shaun L.; Lambkin, Christine L.

    2012-01-01

    Abstract The previously monotypic genus Manestella Metz, 2003 is revised with a single species, Manestella tristriata (Mann, 1933), redescribed and an additional 14 new species described: Manestella caesia sp. n., Manestella campestris sp. n., Manestella canities sp. n., Manestella cooloola sp. n., Manestella fumosa sp. n., Manestella incompleta sp. n., Manestella nubis sp. n., Manestella obscura sp. n., Manestella ocellaris sp. n., Manestella persona sp. n., Manestella poecilothorax sp. n., Manestella umbrapennis sp. n., Manestella vasta sp. n. and Manestella vespera sp. n. The putative sister genus to Manestella, Medomega gen. n., is described containing six new species: Medomega averyi sp. n., Medomega bailmeup sp. n., Medomega chlamydos sp. n., Medomega danielsi sp. n., Medomega gigasathe sp. n., and Medomega nebrias sp. n. Complete taxonomic descriptions were generated from a character matrix developed in Lucid Builder from which natural language descriptions (NLD) were parsed. Images of all species of Manestella and Medomega gen. n. are included, along with dichotomous keys to species. PMID:23226714

  8. Rhopalobdella japonica n. gen., n. sp. (Hirudinea, Piscicolidae) from Dasyatis akajei (Chondrichthyes: Dasyatididae) in the northwestern Pacific.

    PubMed

    Burreson, E M; Kearn, G C

    2000-08-01

    A new genus and species of piscicolid leech in the Platybdellinae inhabits the oral cavity of Dasyatis akajei in the northwestern Pacific Ocean near Tanabe, Japan. The genus Rhopalobdella n. gen. is characterized externally by very small oral and caudal suckers and a smooth body that is widest just posterior to the clitellum. Eyespots and ocelli are lacking. The coelom is spacious with large segmental connecting sinuses between dorsal and ventral sinuses. There are 5 pairs of testisacs, an unusually extensive epididymis, and a very large bursa. Conducting tissue is absent. There are 2 pairs of esophageal diverticula and very well developed nephridia. Rhopalobdella japonica n. gen. n. sp. is characterized by a urosome that tapers strongly to the caudal sucker and by a single gonopore; the common oviduct opens into the posterior portion of the bursa. The coelomic and excretory systems resemble Aestabdella, but in other respects the genera are quite different. This is the first marine leech reported from rays in the northwestern Pacific. PMID:10958442

  9. Gen-2 RFID compatible, zero down-time, programmable mechanical strain-monitors and mechanical impact detectors

    NASA Astrophysics Data System (ADS)

    Chakrabartty, Shantanu; Feng, Tao; Aono, Kenji

    2013-04-01

    A key challenge in structural health monitoring (SHM) sensors embedded inside civil structures is that elec- tronics need to operate continuously such that mechanical events of interest can be detected and appropriately analyzed. Continuous operation however requires a continuous source of energy which cannot be guaranteed using conventional energy scavenging techniques. The paper describes a hybrid energy scavenging SHM sensor which experiences zero down-time in monitoring mechanical events of interest. At the core of the proposed sensor is an analog floating-gate storage technology that can be precisely programmed at nano-watt and pico- watt power levels. This facilitates self-powered, non-volatile data logging of the mechanical events of interest by scavenging energy directly from the mechanical events itself. Remote retrieval of the stored data is achieved using a commercial off-the-shelf Gen-2 radio-frequency identification (RFID) reader which periodically reads an electronic product code (EPC) that encapsulates the sensor data. The Gen-2 interface also facilitates in simultaneous remote access to multiple sensors and also facilitates in determining the range and orientation of the sensor. The architecture of the sensor is based on a token-ring topology which enables sensor channels to be dynamically added or deleted through software control.

  10. A Controller-in-the Loop Simulation of Ground-Based Automated Separation Assurance in a NextGen Environment

    NASA Technical Reports Server (NTRS)

    Homola, J.; Prevot, Thomas; Mercer, Joey S.; Brasil, Connie L.; Martin, Lynne Hazel; Cabrall, C.

    2010-01-01

    A controller-in-the-loop simulation was conducted in the Airspace Operations Laboratory (AOL) at the NASA Ames Research Center to investigate the functional allocation aspects associated with ground-based automated separation assurance in a far-term NextGen environment. In this concept, ground-based automation handled the detection and resolution of strategic and tactical conflicts and alerted the controller to deferred situations. The controller was responsible for monitoring the automation and managing situations by exception. This was done in conditions both with and without arrival time constraints across two levels of traffic density. Results showed that although workload increased with an increase in traffic density, it was still manageable in most situations. The number of conflicts increased similarly with a related increase in the issuance of resolution clearances. Although over 99% of conflicts were resolved, operational errors did occur but were tied to local sector complexities. Feedback from the participants revealed that they thought they maintained reasonable situation awareness in this environment, felt that operations were highly acceptable at the lower traffic density level but were less so as it increased, and felt overall that the concept as it was introduced here was a positive step forward to accommodating the more complex environment envisioned as part of NextGen.

  11. Fervidicella metallireducens gen. nov., sp. nov., a thermophilic, anaerobic bacterium from geothermal waters.

    PubMed

    Ogg, Christopher D; Patel, Bharat K C

    2010-06-01

    A strictly anaerobic, thermophilic bacterium, designated strain AeB(T), was isolated from microbial mats colonizing a run-off channel formed by free-flowing thermal water from a bore well (registered number 17263) of the Great Artesian Basin, Australia. Cells of strain AeB(T) were slightly curved rods (2.5-6.0x1.0 mum) that stained Gram-negative and formed spherical terminal to subterminal spores. The strain grew optimally in tryptone-yeast extract-Casamino acids medium at 50 degrees C (range 37-55 degrees C) and pH 7 (range pH 5-9). Strain AeB(T) grew poorly on yeast extract (0.2 %) and tryptone (0.2 %) as sole carbon sources, which were obligately required for growth on other energy sources. Growth of strain AeB(T) increased in the presence of various carbohydrates and amino acids, but not organic acids. End products detected from glucose fermentation were ethanol, acetate, CO2 and H2. In the presence of 0.2 % yeast extract, iron(III), manganese(IV), vanadium(V) and cobalt(III) were reduced, but not sulfate, thiosulfate, sulfite, elemental sulfur, nitrate or nitrite. Iron(III) was also reduced in the presence of tryptone, peptone, Casamino acids and amyl media (Research Achievement), but not starch, xylan, chitin, glycerol, ethanol, pyruvate, benzoate, lactate, acetate, propionate, succinate, glycine, serine, lysine, threonine, arginine, glutamate, valine, leucine, histidine, alanine, aspartate, isoleucine or methionine. Growth was inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin and NaCl concentrations >2 %. The DNA G+C content was 35.4+/-1 mol%, as determined by the thermal denaturation method. 16S rRNA gene sequence analysis indicated that strain AeB(T) is a member of the family Clostridiaceae, class Clostridia, phylum 'Firmicutes', and is positioned approximately equidistantly between the genera Sarcina, Anaerobacter, Caloramator and Clostridium (16S rRNA gene similarity values of 87.8-90.9 %). On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain AeB(T) is considered to represent a novel species in a new genus, for which the name Fervidicella metallireducens gen. nov., sp. nov. is proposed; the type strain is AeB(T) (=JCM 15555(T)=KCTC 5667(T)). PMID:19671710

  12. Faecalibaculum rodentium gen. nov., sp. nov., isolated from the faeces of a laboratory mouse.

    PubMed

    Chang, Dong-Ho; Rhee, Moon-Soo; Ahn, Sharon; Bang, Byung-Ho; Oh, Ji Eun; Lee, Heung Kyu; Kim, Byoung-Chan

    2015-12-01

    A novel strictly anaerobic strain, ALO17(T), was isolated from mouse faeces and found to produce lactic acid as a major metabolic end product. The isolate was observed to be Gram-stain positive, non-motile, non-spore forming small rods, oxidase and catalase negative, and to form cream-coloured colonies on DSM 104 agar plates. The NaCl range for growth was determined to be 0-2 % (w/v). The isolate was found to grow optimally at 37 °C, with 0.5 % (w/v) NaCl and at pH 7. The cell wall hydrolysates were found to contain ribose as a major sugar. The genomic DNA G+C content was determined to be 52.3 mol%. A phylogenetic analysis of the 16S rRNA gene sequence revealed that Holdemanella biformis DSM 3989(T), Faecalicoccus pleomorphus ATCC 29734(T), Faecalitalea cylindroides ATCC 27803(T), and Allobaculum stercoricanis DSM 13633(T) are closely related to the isolate (87.4, 87.3, 86.9 and 86.9 % sequence similarity), respectively. The major cellular fatty acids (>10 %) of the isolate were identified as C18:1 cis 9 FAME (36.9 %), C16:0 FAME (33.7 %) and C18:0 FAME (13.2 %). In contrast to the tested reference strains, C20:0 FAME (4.0 %) was detected only in strain ALO17(T) whilst C16:0 DMA was absent. The isolate also differed in its substrate oxidation profiles from the reference strains by being positive for D-melibiose and stachyose but negative for N-acetyl-D-galactosamine and 3-methyl-D-glucose. On the basis of polyphasic taxonomic evidence from this study, the isolate is concluded to belong to a novel genus within the family Erysipelothricaceae. We propose the name Faecalibaculum rodentium gen. nov., sp. nov. to accommodate strain ALO17(T) (=KCTC 15484(T) = JCM 30274(T)) as the type strain. PMID:26349481

  13. Telmatocola sphagniphila gen. nov., sp. nov., a Novel Dendriform Planctomycete from Northern Wetlands

    PubMed Central

    Kulichevskaya, Irina S.; Serkebaeva, Yulia M.; Kim, Yongkyu; Rijpstra, W. Irene C.; Damsté, Jaap S. Sinninghe; Liesack, Werner; Dedysh, Svetlana N.

    2012-01-01

    Members of the phylum Planctomycetes are common inhabitants of northern wetlands. We used barcoded pyrosequencing to survey bacterial diversity in an acidic (pH 4.0) Sphagnum peat sampled from the peat bog Obukhovskoye, European North Russia. A total of 21189 bacterial 16S rRNA gene sequences were obtained, of which 1081 reads (5.1%) belonged to the Planctomycetes. Two-thirds of these sequences affiliated with planctomycete groups for which characterized representatives have not yet been available. Here, we describe two organisms from one of these previously uncultivated planctomycete groups. One isolate, strain OB3, was obtained from the peat sample used in our molecular study, while another strain, SP2T (=DSM 23888T?=?VKM B-2710T), was isolated from the peat bog Staroselsky moss. Both isolates are represented by aerobic, budding, pink-pigmented, non-motile, spherical cells that are arranged in unusual, dendriform-like structures during growth on solid media. These bacteria are moderately acidophilic and mesophilic, capable of growth at pH 4.0–7.0 (optimum pH 5.0–5.5) and at 6–30°C (optimum 20–26°C). The preferred growth substrates are various heteropolysaccharides and sugars, the latter being utilized only if provided in low concentrations (?0.025%). In contrast to other described planctomycetes, strains SP2T and OB3 possess weak cellulolytic potential. The major fatty acids are C16:1?5c, C18:1?5c, C16:0, and C18:0. Characteristic lipids are the n-C31 polyunsaturated alkene (9–10 double bonds) and C30:1/C32:1 (?-1) hydroxy fatty acids. The G?+?C content of the DNA is 58.5–59.0?mol%. Strains SP2T and OB3 share identical 16S rRNA gene sequences, which exhibit only 86 and 87% similarity to those of Gemmata obscuriglobus and Zavarzinella formosa. Based on the characteristics reported here, we propose to classify these novel planctomycetes as representatives of a novel genus and species, Telmatocola sphagniphila gen. nov., sp. nov. PMID:22529844

  14. Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop.

    PubMed

    Li, Leilei; Praet, Jessy; Borremans, Wim; Nunes, Olga C; Manaia, Célia M; Cleenwerck, Ilse; Meeus, Ivan; Smagghe, Guy; De Vuyst, Luc; Vandamme, Peter

    2015-01-01

    In the frame of a bumble bee gut microbiota study, acetic acid bacteria (AAB) were isolated using a combination of direct isolation methods and enrichment procedures. MALDI-TOF MS profiling of the isolates and a comparison of these profiles with profiles of established AAB species identified most isolates as Asaia astilbis or as 'Commensalibacter intestini', except for two isolates (R-52486 and LMG 28161(T)) that showed an identical profile. A nearly complete 16S rRNA gene sequence of strain LMG 28161(T) was determined and showed the highest pairwise similarity to Saccharibacter floricola S-877(T) (96.5%), which corresponded with genus level divergence in the family Acetobacteraceae. Isolate LMG 28161(T) was subjected to whole-genome shotgun sequencing; a 16S-23S rRNA internal transcribed spacer (ITS) sequence as well as partial sequences of the housekeeping genes dnaK, groEL and rpoB were extracted for phylogenetic analyses. The obtained data confirmed that this isolate is best classified into a new genus in the family Acetobacteraceae. The DNA G+C content of strain LMG 28161(T) was 54.9 mol%. The fatty acid compositions of isolates R-52486 and LMG 28161(T) were similar to those of established AAB species [with C18:1?7c (43.1%) as the major component], but the amounts of fatty acids such as C19:0 cyclo ?8c, C14:0 and C14:0 2-OH enabled to differentiate them. The major ubiquinone was Q-10. Both isolates could also be differentiated from the known genera of AAB by means of biochemical characteristics, such as their inability to oxidize ethanol to acetic acid, negligible acid production from melibiose, and notable acid production from d-fructose, sucrose and d-mannitol. In addition, they produced 2-keto-d-gluconate, but not 5-keto-d-gluconate from d-glucose. Therefore, the name Bombella intestini gen nov., sp. nov. is proposed for this new taxon, with LMG 28161(T) (?=DSM 28636(T)?=R-52487(T)) as the type strain of the type species. PMID:25336723

  15. Desmozoon lepeophtherii n. gen., n. sp., (Microsporidia: Enterocytozoonidae) infecting the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae)

    PubMed Central

    2009-01-01

    Background A microsporidian was previously reported to infect the crustacean parasite, Lepeophtheirus salmonis (Krøyer, 1837) (Copepoda, Caligidae), on farmed Atlantic salmon (Salmo salar L.) in Scotland. The microsporidian was shown to be a novel species with a molecular phylogenetic relationship to Nucleospora (Enterocytozoonidae), but the original report did not assign it to a genus or species. Further studies examined the development of the microsporidian in L. salmonis using electron microscopy and re-evaluated the molecular findings using new sequence data available for the group. Here we report a full description for the microsporidian and assign it to a new genus and species. Results The microsporidian infects subcuticular cells that lie on the innermost region of the epidermal tissue layer beneath the cuticle and along the internal haemocoelic divisions. The mature spores are sub-spherical with a single nucleus and an isofilar polar filament with 5-8 turns in a double coil. The entire development is in direct contact with the host cell cytoplasm and is polysporous. During early merogony, a diplokaryotic nuclear arrangement exists which is absent throughout the rest of the developmental cycle. Large merogonial plasmodia form which divide to form single uninucleate sporonts. Sporogonial plasmodia were not observed; instead, binucleate sporonts divide to form two sporoblasts. Prior to final division, there is a precocious development of the polar filament extrusion apparatus which is associated with large electron lucent inclusions (ELIs). Analyses of DNA sequences reveal that the microsporidian is robustly supported in a clade with other members of the Enterocytozoonidae and confirms a close phylogenetic relationship with Nucleospora. Conclusion The ultrastructural findings of the precocious development of the polar filament and the presence of ELIs are consistent with those of the Enterocytozoonidae. However, the confirmed presence of an early diplokaryotic stage and a merogonial plasmodium that divides to yield uninucleate sporonts instead of transforming into a sporogonial syncitium, are features not currently associated with the family. Yet, analyses of DNA sequence data clearly place the microsporidian within the Enterocytozoonidae. Therefore, due to the novelty of the copepod host, the ultrastructural findings and the robust nature of the phylogenetic analyses, a new genus should be created within the Enterocytozoonide; Desmozoon lepeophtherii n. gen. n. sp. is proposed. PMID:19943930

  16. Halocalculus aciditolerans gen. nov., sp. nov., an acid-tolerant haloarchaeon isolated from commercial salt.

    PubMed

    Minegishi, Hiroaki; Echigo, Akinobu; Kuwahara, Ai; Shimane, Yasuhiro; Kamekura, Masahiro; Itoh, Takashi; Ohkuma, Moriya; Usami, Ron

    2015-05-01

    Three halophilic archaeal strains, MH2-243-1(T), MH2-93-1 and MH2-91-1 were isolated from commercial salt samples from Japan, Australia, and Bolivia. Strain MH2-243-1(T) was able to grow in the presence of 12-30% (w/v) NaCl (optimum, 18% NaCl), at pH 4.5-7.0 (optimum, pH 6.0) and at 20-60 °C (optimum, 40 °C). Strains MH2-91-1 and MH2-93-1 grew in slightly different ranges. The orthologous 16S rRNA gene sequences of the three strains were almost identical (99.8-99.9% similarities), and the closest relative was Salarchaeum japonicum JCM 16327(T) with 94.2-94.3% 16S rRNA gene sequence similarities, followed by strains of members of the closely related genera Halobacterium and Halarchaeum . The RNA polymerase subunit B' gene (rpoB') sequence also showed the highest similarity (86.6%) to that of Salarchaeum japonicum JCM 16327(T). The DNA G+C contents of strains MH2-243-1(T), MH2-93-1 and MH2-91-1 were 68.5, 68.8 and 68.3 mol%, respectively. DNA-DNA relatedness values amongst the three strains were 97-99%. The polar lipids of the three strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, and at least seven unidentified glycolipids. The polar lipid composition differed from those of Salarchaeum japonicum and species of the genera Halobacterium and Halarchaeum . Based on the phenotypic and phylogenetic analyses, it is proposed that the isolates represent a novel species of a new genus, for which the name Halocalculus aciditolerans gen. nov., sp. nov. is proposed. The type strain of the type species is MH2-243-1(T) (?=?JCM 19596(T)?=KCTC 4149(T)) isolated from solar salt produced in Japan. MH2-93-1 (?=?JCM 19595) and MH2-91-1 (?=?JCM 19594) are additional strains of the type species. PMID:25721724

  17. Epibacterium ulvae gen. nov., sp. nov., epibiotic bacteria isolated from the surface of a marine alga.

    PubMed

    Penesyan, Anahit; Breider, Sven; Schumann, Peter; Tindall, Brian J; Egan, Suhelen; Brinkhoff, Thorsten

    2013-05-01

    Two Gram-reaction-negative, rod-shaped, motile bacteria, designated strains U82 and U95(T), were isolated from the marine alga Ulva australis collected at Sharks Point, Clovelly, a rocky intertidal zone near Sydney, Australia. Both strains were oxidase- and catalase-positive, formed brown- to black-pigmented colonies and required NaCl for growth. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that these strains belong to the Roseobacter clade within the Alphaproteobacteria. The 16S rRNA genes of both strains were identical across the sequenced 1326 nt, but showed differences in the intergenic spacer region (ITS) between the 16S and the 23S rRNA genes. At the genomic level the DNA G+C contents of strains U82 and U95(T) were identical (52.6?mol%) and they had a DNA-DNA hybridization value of 83.7%, suggesting that these strains belong to the same species. The closest described phylogenetic neighbour to strains U82 and U95(T) was Thalassobius aestuarii DSM 15283(T) with 95.8% 16S rRNA gene sequence similarity. Other close relatives include further species of the genera Thalassobius and Shimia. Strains U82 and U95(T) were negative for bacteriochlorophyll a production, showed antibacterial activity towards other marine bacteria, were resistant to the antibiotics gentamicin and spectinomycin and were unable to hydrolyse starch or gelatin. The major fatty acids (>1%) were 18?:?1?7c, 16?:?0, 18?:?2, 10?:?0 3-OH, 12?:?0, 20?:?1 2-OH and 18?:?0. The polar lipid pattern indicated the presence of phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and four unidentified phospholipids. Both strains produced ubiquinone 10 (Q-10) as the sole respiratory lipoquinone. Based on their phenotypic and phylogenetic characteristics, it is suggested that strains U82 and U95(T) are members of a novel species within a new genus for which the name Epibacterium ulvae gen. nov., sp. nov. is proposed. The type strain of the type species is U95(T) (?=?DSM 24752(T)?=?LMG 26464(T)). PMID:22904216

  18. GENetic and clinical Predictors Of treatment response in Depression: the GenPod randomised trial protocol

    PubMed Central

    Thomas, Laura; Mulligan, Jean; Mason, Victoria; Tallon, Debbie; Wiles, Nicola; Cowen, Philip; Nutt, David; O'Donovan, Michael; Sharp, Deborah; Peters, Tim; Lewis, Glyn

    2008-01-01

    Background The most effective pharmacological treatments for depression inhibit the transporters that reuptake serotonin (Selective Serotonin Reuptake Inhibitors – SSRIs) and noradrenaline (Noradrenaline Reuptake Inhibitors – NaRIs) into the presynaptic terminal. There is evidence to suggest that noradrenaline and serotonin enhancing drugs work through separate mechanisms to produce their clinical antidepressant action. Although most of the current evidence suggests there is little difference in overall efficacy between SSRIs and NaRIs, there are patients who respond to one class of compounds and not another. This suggests that treatment response could be predicted by genetic and/or clinical characteristics. Firstly, this study aims to investigate the influence of a polymorphism (SLC6A4) in the 5HT transporter in altering response to SSRI medication. Secondly, the study will investigate whether those with more severe depression have a better response to NaRIs than SSRIs. Methods/design The GenPod trial is a multi-centre randomised controlled trial. GPs referred patients aged between 18–74 years presenting with a new episode of depression, who did not have any medical contraindications to antidepressant medication and who had no history of psychosis or alcohol/substance abuse. Patients were interviewed to ascertain their suitability for the study. Eligible participants (with a primary diagnosis of depression according to ICD10 criteria and a Beck Depression Inventory (BDI) score > 14) were randomised to receive one of two antidepressant treatments, either the SSRI Citalopram or the NaRI Reboxetine, stratified according to severity. The final number randomised to the trial was 601. Follow-up assessments took place at 2, 6 and 12 weeks following randomisation. Primary outcome was measured at 6 weeks by the BDI. Outcomes will be analysed on an intention-to-treat basis and will use multiple regression models to compare treatments. Discussion The results of the trial will provide information about targeting antidepressant treatment for individual patients; in turn this may increase prescribing efficacy, thereby speeding recovery and reducing the cost to the NHS. It will also help to understand the different roles that noradrenaline and serotonin might play in the biology of depression. The trial is expected to report in the autumn of 2008. Trial Registration ISRCTN 31345163 PMID:18498636

  19. Gender difference in diastolic function in hypertension (the HyperGEN study).

    PubMed

    Bella, Jonathan N; Palmieri, Vittorio; Kitzman, Dalane W; Liu, Jennifer E; Oberman, Albert; Hunt, Steven C; Hopkins, Paul N; Rao, D C; Arnett, Donna K; Devereux, Richard B

    2002-05-01

    Although several studies indicate that there are gender differences in left ventricular (LV) systolic function, it remains unclear whether similar differences exist with regard to diastolic function. Accordingly, Doppler echocardiograms were analyzed in 515 male and 839 female, mostly treated (95%) hypertensive participants enrolled in the Hypertension Genetic Epidemiology Network (HyperGEN) study with no evidence of abnormal wall motion or significant valvular heart disease. There was no difference in age between genders, but after adjusting for age and race, men had lower body mass indexes (29.8 +/- 5.2 vs 32.3 +/- 7.6 kg/m(2)) and heart rates (67 +/- 12 vs 69 +/- 11 beats/min) and higher systolic and diastolic blood pressures (BP) than women (134 +/- 20 vs 130 +/- 21 and 80 +/- 11 vs 72 +/- 11 mm Hg, all p <0.001). LV mass/height(2.7) was slightly greater in women than in men (43 +/- 10 vs 42 +/- 9 g/m(2.7), p <0.05). After adjusting for age, race, systolic BP, body mass index, heart rate, and LV hypertrophy, both mitral E-wave (70 +/- 18 vs 77 +/- 19) and A-wave (74 +/- 15 vs 79 +/- 17, both p <0.001) velocities were lower in men than in women, but the mitral E/A ratio and atrial filling fraction were nearly identical in both genders. Deceleration time (221 +/- 55 vs 214 +/- 46 cm/s, p = 0.018) and isovolumic relaxation time (IVRT) were longer in men than in women (85 +/- 18 vs 81 +/- 17 cm/s, p <0.001). Prolonged IVRT was present in more men than women (14% vs 7%, p <0.05). In analyses of covariance, adjusting for age, race, systolic BP, body mass index, heart rate, and medications, male gender remained related to prolonged deceleration time and IVRT. Thus, in this population-based sample of hypertensive adults, men had evidence of slower early diastolic LV filling than women. This gender difference in diastolic function may provide insight into gender differences in congestive heart failure and other specific cardiovascular diseases. PMID:11988194

  20. Session B--Maintenance of Key Biodiversity Attributes--Gray, Blackwell USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 49

    E-print Network

    Session B--Maintenance of Key Biodiversity Attributes--Gray, Blackwell USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 49 The Maintenance of Key Biodiversity Attributes Through Ecosystem Restoration Operations1 Robert W. Gray2 and Bruce A. Blackwell3 Abstract The requirement to manage for key

  1. Thomas, Robert B. 1989. Piecewise SALT sampling for estimating suspended sediment yields. Gen. Tech. Rep. PSW-114. Berkeley, CA: Pacific Southwest Forest and Range

    E-print Network

    , probability sampling, measurement, SALT sampling Forest activities such as logging, road building, and mining#12;Thomas, Robert B. 1989. Piecewise SALT sampling for estimating suspended sediment yields. Gen, U.S. Department of Agriculture; 11 p. A probability sampling method called SALT (Selection At List

  2. Film and Language Learning in Victorian Schools: A Study of the 2009 Next Gen Program of the "Melbourne International Film Festival"

    ERIC Educational Resources Information Center

    Lo Bianco, Hana

    2010-01-01

    This article investigates the role of film in language education based on a study of the 2009 "Melbourne International Film Festival" (MIFF). It is structured around a literature review and results from surveys of students and teachers who participated in the young people's section of the program, Next Gen. The article argues that film can provide…

  3. Session H--NEPA Disclosure of Air Quality Impacts--Ahuja, Perrot USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008.

    E-print Network

    air quality and has the potential to impact human health and quality of life. Public concern aboutSession H--NEPA Disclosure of Air Quality Impacts--Ahuja, Perrot USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. . 193 National Environmental Policy Act Disclosure of Air Quality Impacts

  4. and solvent in ion permeation. J. Gen. Physiol. (in the press). 16. Aqvist, J. & Luzhkov, V. Ion permeation mechanism of the potassium channel. Nature 404, 881884

    E-print Network

    Kah, Linda

    and solvent in ion permeation. J. Gen. Physiol. (in the press). 16. A°qvist, J. & Luzhkov, V. Ion, 8191­8204 (2000). 19. Berne`che, S. & Roux, B. Energetics of ion conduction through the Kþ channel. Nature 414, 73­77 (2001). 20. Berne`che, S. & Roux, B. A microscopic view of ion conduction through

  5. Session E--Short-Term Effects of Wildfires on Fishes--Rinne, Carter USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 167

    E-print Network

    Session E--Short-Term Effects of Wildfires on Fishes--Rinne, Carter USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 167 Short-Term Effects of Wildfires on Fishes in the Southwestern United was a season of markedly increased wildfire in the southwestern United States. Four fires affected landscapes

  6. USDA Forest Service Gen. Tech. Rep. PSW-GTR-168-Web. 1998. 55 Evaluating the Impacts of Logging Activities on Erosion

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-168-Web. 1998. 55 Evaluating the Impacts of Logging station (NFC) was used as a control to evaluate the effects of logging in the South Fork, in the 1970's percent over the total predicted for a 6-yr period commencing with the onset of logging. When the roles

  7. Session C--Effects of Fire on Soil Properties and Sediment Fluxes--Wohlgemuth, Hubbert USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 115

    E-print Network

    Experimental Forest provided an opportunity to quantify the effects of fire on soil hydrologic propertiesSession C--Effects of Fire on Soil Properties and Sediment Fluxes--Wohlgemuth, Hubbert USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 115 The Effects of Fire on Soil Hydrologic Properties

  8. 29USDA Forest Service Gen. Tech. Rep. PSW-GTR-155. 1996. Statistical Considerations for Plot Design, Sampling Procedures, Analysis... Arbaugh and Bednar

    E-print Network

    29USDA Forest Service Gen. Tech. Rep. PSW-GTR-155. 1996. Statistical Considerations for Plot Design present recommendations in this chapter to develop plot design and sampling strategies that follow. The specific questions will be addressed about plot design, the method used to locate plots, and the optimal

  9. 105USDA Forest Service Gen.Tech.Rep. PSW-GTR-166. 1998. Nitrogenous (N) air pollutant concentrations and surface deposition of nitrate (NO3

    E-print Network

    determination of gaseous and particulate N pollutants. These systems have been successfully used in chaparral results of a study that monitored concentrations of gaseous and particulate N air pollutants; measured105USDA Forest Service Gen.Tech.Rep. PSW-GTR-166. 1998. Abstract Nitrogenous (N) air pollutant

  10. 281USDA Forest Service Gen.Tech.Rep. PSW-GTR-166. 1998. Systematic assessment and observation (survey, inventory) of forests in Latvia has been underway since the

    E-print Network

    281USDA Forest Service Gen.Tech.Rep. PSW-GTR-166. 1998. Abstract Systematic assessment and observation (survey, inventory) of forests in Latvia has been underway since the 1700's. Latvia's forests are in the boreal/temperate forest zone and cover 44 percent of the country. Forest growing conditions

  11. Session D--Geographic Variation in Mixed Conifer Fire Regimes--Beaty, Taylor USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 123

    E-print Network

    Session D--Geographic Variation in Mixed Conifer Fire Regimes--Beaty, Taylor USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 123 Geographic Variation in Mixed-Conifer Forest Fire Regimes on geographic variability in mixed conifer (MC) forest fire regimes. MC forests are typically described

  12. 73USDAForestServiceGen.Tech.Rep.PSW-GTR-166.1998. Ozone concentrations have been monitored at the Glacier Lakes Ecosystem Experiment Site (GLEES) in the Snowy

    E-print Network

    layer conductances, canopy conductances and photosynthesis rates to ambient ozone concentrations73USDAForestServiceGen.Tech.Rep.PSW-GTR-166.1998. Abstract Ozone concentrations have been monitored of a mature subalpine forest near timberline. Continuous ozone and meteorological monitoring are a part

  13. Session D--A Neutral Model of Low-Severity Fire Regimes--McKenzie, Hessl USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 139

    E-print Network

    Session D--A Neutral Model of Low-Severity Fire Regimes--McKenzie, Hessl USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 139 A Neutral Model for Low-Severity Fire Regimes1 Don McKenzie2 and Amy null, or neutral, model, characteristics of natural fire regimes estimated from fire history data can

  14. Gen. Tech. Rep. PSW-58. Berkeley, CA: Pacific Southwest Forest and Range Experiment Station, Forest Service, U.S. Department of Agriculture; 1982. 345

    E-print Network

    Gen. Tech. Rep. PSW-58. Berkeley, CA: Pacific Southwest Forest and Range Experiment Station, Forest Scientist, USDA Forest Ser- vice, Rocky Mountain Forest and Range Experiment Station located at the Station, space permits discussing only a few general activ- ities and their impacts. Managers can either

  15. Poster Session--Fuel Consumption During Prescribed Fires in Big Sage--Wright, Ottmar USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 363

    E-print Network

    Poster Session--Fuel Consumption During Prescribed Fires in Big Sage--Wright, Ottmar USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 363 Fuel Consumption During Prescribed Fires in Big Sage of operational prescribed fires in big sage (Artemisia tridentata) ecosystems throughout the interior West. Pre

  16. 75 FR 27332 - AER NY-Gen, LLC; Eagle Creek Hydro Power, LLC; Eagle Creek Water Resources, LLC; Eagle Creek Land...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-14

    ... Energy Regulatory Commission AER NY-Gen, LLC; Eagle Creek Hydro Power, LLC; Eagle Creek Water Resources... Creek Hydro Power, LLC, Eagle Creek Water Resources, LLC, and Eagle Creek Land Resources, LLC.... For the transferee: Mr. Paul Ho, Eagle Creek Hydro Power, LLC, Eagle Creek Water Resources, LLC,...

  17. 77 FR 13592 - AER NY-Gen, LLC; Eagle Creek Hydro Power, LLC, Eagle Creek Water Resources, LLC, Eagle Creek Land...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-07

    ... Energy Regulatory Commission AER NY-Gen, LLC; Eagle Creek Hydro Power, LLC, Eagle Creek Water Resources... Power, LLC, Eagle Creek Water Resources, LLC, and Eagle Creek Land Resources, LLC (transferees) filed an... Resources, LLC, and Eagle Creek Land Resources, LLC, 65 Madison Avenue, Morristown, NJ 07960, (973)...

  18. Poster Session--Debris Flow Occurrence--May, Lee USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008.342

    E-print Network

    Poster Session--Debris Flow Occurrence--May, Lee USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008.342 Debris Flow Occurrence in the Immediate Postfire and Interfire Periods and Associated Effects rates of landslide and debris flow activity due to a loss of root strength and vegetative cover

  19. Poster Session--Predicting Patterns of Alien Plant Invasion--Underwood, Klinger, Moore USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 361

    E-print Network

    Poster Session--Predicting Patterns of Alien Plant Invasion--Underwood, Klinger, Moore USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 361 Predicting Patterns of Alien Plant Invasions in Areas of alien plant species. This is particularly problematic in areas which have experienced disturbances

  20. Session L--Effects of Fire on Serpentine Vegetation--Safford, Harrison USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 321

    E-print Network

    Session L--Effects of Fire on Serpentine Vegetation--Safford, Harrison USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 321 The Effects of Fire on Serpentine Vegetation and Implications fire effects on adjacent serpentine and non-serpentine soils in two vegetation types, grassland

  1. GenAge: a genomic and proteomic network map of human ageing Jo~ao Pedro de Magalh~aes*, Olivier Toussaint

    E-print Network

    de Magalhães, João Pedro

    GenAge: a genomic and proteomic network map of human ageing Jo~ao Pedro de Magalh~aes*, Olivier ageing. Moreover, we rendered the first proteomic network map of human ageing, which suggests these genes fit together and impact on human ageing. The only few genes shown to influence human ageing

  2. Poster Session--Prescribed Fire Effects on California's Oaks--Paysen USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008.352

    E-print Network

    Poster Session--Prescribed Fire Effects on California's Oaks--Paysen USDA Forest Service Gen. Tech. Figure 1--Post fire erosion problem. Figure 2--U.S. Forest Service prescribed burning program. 1 A poster 92507. e-mail: tpaysen@fs.fed.us. #12;Poster Session--Prescribed Fire Effects on California's Oaks

  3. Session C--Effects of Mulch Treatments--Riechers, Beyers, Robichaud, Jennings, Kreutz, Moll USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 107

    E-print Network

    effectiveness in reducing erosion compared to straw. Introduction Applying mulch to protect bare groundSession C--Effects of Mulch Treatments--Riechers, Beyers, Robichaud, Jennings, Kreutz, Moll USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 107 Effects of Three Mulch Treatments on Initial

  4. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 395 Anderson, Daniel W.; Jehl, Joseph R., Jr.; Risebrough, R.W.; Woods,

    E-print Network

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 395 Anderson, Daniel W.; Jehl, Joseph R., Jr. 1979. The adaptive significance of the reproductive pattern in the Black Guillemot Cepphus grylle. The Black Noddy Anous tenuirostris on Ascension Island. Part 1. Ibis 103b:235-273. Ashmole, N.P. 1971. Avian

  5. Session B--Small-Diameter Timber Alchemy--Fried, Barbour, Fight, Christensen, Pinjuv USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 29

    E-print Network

    Session B--Small-Diameter Timber Alchemy--Fried, Barbour, Fight, Christensen, Pinjuv USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 29 Small-Diameter Timber Alchemy: Can Utilization Pay the Way- mail: Jeremy.Fried@fs.fed.us. #12;Session B--Small-Diameter Timber Alchemy--Fried, Barbour, Fight

  6. 35USDA Forest Service Gen. Tech. Rep. PSW-GTR-155. 1996. Establishment of Monitoring Plots and Evaluation of Trees Injured by Ozone Duriscoe, Stolte, and Pronos

    E-print Network

    ParkService,ThreeRiv- ers, CA 93271; Deputy Director, ForestHealthMonitoring,South- ern Experiment Station, USDA Forest35USDA Forest Service Gen. Tech. Rep. PSW-GTR-155. 1996. Establishment of Monitoring Plots, Stanislaus National Forest, USDA Forest Service, 19777 Greenley Rd., Sonora, CA 95370 2Trade names

  7. 327USDA Forest Service Gen.Tech.Rep. PSW-GTR-166. 1998. Effective management of forest resources requires access to current and consistent geospatial information

    E-print Network

    327USDA Forest Service Gen.Tech.Rep. PSW-GTR-166. 1998. Abstract Effective management of forest contribution to the geospatial information needed in the USDA Forest Service (FS). Remote sensing is a source- ers determine changes in land cover over time. This paper examines the ability to integrate remote

  8. CHROMOSOMAL MAPPING OF 12 GENE-ASSOCIATED MARKERS IN CATTLE IDENTIFIES NOVEL REGIONS OF CONSERVED SYNTENY BETWEEN THE HUMAN AND BOVINE GEN0MES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Current gene density on the bovine genetic maps is extremely limited and the resolution of the human-bovine comparative map is insufficient for selection of positional candidate genes controlling many economic traits of interest in dairy cattle. This study describes the chromosomal mapping of 12 gen...

  9. 271USDA Forest Service Gen.Tech.Rep. PSW-GTR-166. 1998. Forests in the Ukraine are affected by environmental pollution, intensive forestry practice, and recreational

    E-print Network

    271USDA Forest Service Gen.Tech.Rep. PSW-GTR-166. 1998. Abstract Forests in the Ukraine Pollution Effects on Forests (ICP-Forests). A network of monitoring plots has been established in 14 Program -- defoliation and discoloration of forest stands -- have been observed on 215 plots. Data

  10. 55USDA Forest Service Gen. Tech. Rep. PSW-GTR-158. 1995. FARSITE: A Fire Area Simulator for Fire Managers1

    E-print Network

    55USDA Forest Service Gen. Tech. Rep. PSW-GTR-158. 1995. FARSITE: A Fire Area Simulator for Fire models based on "cellular automata" that spread fire as a contagion process between cells of a regular). The cellular automata approach has been pursued by many researchers, too numerous to mention here. Models based

  11. Session I--Fire Management Over Large Landscapes --Boykin USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 201

    E-print Network

    million acres (White Sands Missile Range) into parcels useful in fire management. Within this hierarchy, 8 ecology on White Sands Missile Range (WSMR) and the deserts of the southwestern United States. This paper Landscapes--Boykin USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008.202 Study Area White Sands Missile

  12. Session D--Ecology of Fire on White Sands Missile Range--Boykin USDA Forest Service Gen. Tech. Rep. PSW-GTR-189 2008. 131

    E-print Network

    Session D--Ecology of Fire on White Sands Missile Range--Boykin USDA Forest Service Gen. Tech. Rep. PSW-GTR-189 2008. 131 Response of Selected Plants to Fire on White Sands Missile Range, New Mexico1 related to many plants and communities within White Sands Missile Range. I began by identifying the known

  13. Membrane topology screen of secondary transport proteins in structural class ST[3] of the MemGen classification. Confirmation and structural diversity.

    PubMed

    ter Horst, Ramon; Lolkema, Juke S

    2012-01-01

    The MemGen structural classification of membrane proteins groups families of proteins by hydropathy profile alignment. Class ST[3] of the MemGen classification contains 32 families of transporter proteins including the IT superfamily. Transporters from 19 different families in class ST[3] were evaluated by the TopScreen experimental topology screening method to verify the structural classification by MemGen. TopScreen involves the determination of the cellular disposition of three sites in the polypeptide chain of the proteins which allows for discrimination between different topology models. For nearly all transporters at least one of the predicted localizations is different in the models produced by MemGen and predictor TMHMM. Comparison to the experimental data showed that in all cases the prediction by MemGen was correct. It is concluded that the structural model available for transporters of the [st324]ESS and [st326]2HCT families is also valid for the other families in class ST[3]. The core structure of the model consists of two homologous domains, each containing 5 transmembrane segments, which have an opposite orientation in the membrane. A reentrant loop is present in between the 4th and 5th segments in each domain. Nearly all of the identified and experimentally confirmed structural variations involve additions of transmembrane segments at the boundaries of the core model, at the N- and C-termini or in between the two domains. Most remarkable is a domain swap in two subfamilies of the [st312]NHAC family that results in an inverted orientation of the proteins in the membrane. PMID:21983116

  14. Mooreia alkaloidigena gen. nov., sp. nov. and Catalinimonas alkaloidigena gen. nov., sp. nov., alkaloid-producing marine bacteria in the proposed families Mooreiaceae fam. nov. and Catalimonadaceae fam. nov. in the phylum Bacteroidetes

    PubMed Central

    Choi, Eun Ju; Beatty, Deanna S.; Paul, Lauren A.; Fenical, William

    2013-01-01

    Bacterial strains CNX-216T and CNU-914T were isolated from marine sediment samples collected from Palmyra Atoll and off Catalina Island, respectively. Both strains were Gram-negative and aerobic and produce deep-orange to pink colonies and alkaloid secondary metabolites. Cells of strain CNX-216T were short, non-motile rods, whereas cells of strain CNU-914T were short, curved rods with gliding motility. The DNA G+C contents of CNX-216T and CNU-914T were respectively 57.7 and 44.4 mol%. Strains CNX-216T and CNU-914T contained MK-7 as the predominant menaquinone and iso-C15?:?0 and C16?:?1?5c as the major fatty acids. Phylogenetic analyses revealed that both strains belong to the order Cytophagales in the phylum Bacteroidetes. Strain CNX-216T exhibited low 16S rRNA gene sequence identity (87.1?%) to the nearest type strain, Cesiribacter roseus 311T, and formed a well-supported lineage that is outside all currently described families in the order Cytophagales. Strain CNU-914T shared 97.6?% 16S rRNA gene sequence identity with ‘Porifericola rhodea’ N5EA6-3A2B and, together with ‘Tunicatimonas pelagia’ N5DB8-4 and four uncharacterized marine bacteria isolated as part of this study, formed a lineage that is clearly distinguished from other families in the order Cytophagales. Based on our polyphasic taxonomic characterization, we propose that strains CNX-216T and CNU-914T represent novel genera and species, for which we propose the names Mooreia alkaloidigena gen. nov., sp. nov. (type strain CNX-216T ?=?DSM 25187T ?=?KCCM 90102T) and Catalinimonas alkaloidigena gen. nov., sp. nov. (type strain CNU-914T ?=?DSM 25186T ?=?KCCM 90101T) within the new families Mooreiaceae fam. nov. and Catalimonadaceae fam. nov. PMID:22753528

  15. Reclassification of Alcaligenes latus strains IAM 12599T and IAM 12664 and Pseudomonas saccharophila as Azohydromonas lata gen. nov., comb. nov., Azohydromonas australica sp. nov. and Pelomonas saccharophila gen. nov., comb. nov., respectively.

    PubMed

    Xie, Cheng-Hui; Yokota, Akira

    2005-11-01

    The aim of this study was to clarify the taxonomic position of the nitrogen-fixing and hydrogen-oxidizing bacteria Alcaligenes latus strains IAM 12599T, IAM 12664 and IAM 12665 and Pseudomonas saccharophila IAM 14368T. It was found that the type strain of Alcaligenes latus, IAM 12599T, showed 99 x 9 and 96 x 1 % 16S rRNA gene sequence similarity to strains IAM 12665 and IAM 12664, respectively. A comparison using DNA-DNA hybridization suggested that strains IAM 12599T and IAM 12665 belong to a single species (89 x 7 %) and that strain IAM 12664 (35 x 1 %) forms a separate species. The phenotypic characteristics also support the conclusion that these bacteria should be identified as two species of a new genus: Azohydromonas lata gen. nov., comb. nov. (type strain IAM 12599T=DSM 1122T=LMG 3321T=ATCC 29712T; reference strain IAM 12665=DSM 1123=LMG 3325=ATCC 29714) and Azohydromonas australica sp. nov. (type strain IAM 12664T=DSM 1124T=LMG 3324T=ATCC 29713T). Pseudomonas saccharophila IAM 14368T was found to be closely related to the phototrophic bacterium Roseateles depolymerans, with 96 x 8 % 16S rRNA gene sequence similarity, but the two bacteria are quite different with respect to their metabolism and some significant phenotypic characteristics, suggesting that they cannot be included in a single genus. Further studies on their nifH gene sequences, G+C content of the DNA and cellular fatty acid composition confirm that Pseudomonas saccharophila should be reclassified: the name Pelomonas saccharophila gen. nov., comb. nov. is proposed, with the type strain IAM 14368T (=LMG 2256T=ATCC 15946T). PMID:16280506

  16. Progress reports for Gen IV sodium fast reactor activities FY 2007.

    SciTech Connect

    Cahalan, J. E.; Tentner, A. M.; Nuclear Engineering Division

    2007-10-04

    An important goal of the US DOE Sodium Fast Reactor (SFR) program is to develop the technology necessary to increase safety margins in future fast reactor systems. Although no decision has been made yet about who will build the next demonstration fast reactor, it seems likely that the construction team will include a combination of international companies, and the safety design philosophy for the reactor will reflect a consensus of the participating countries. A significant amount of experience in the design and safety analysis of Sodium Fast Reactors (SFR) using oxide fuel has been developed in both Japan and France during last few decades. In the US, the traditional approach to reactor safety is based on the principle of defense-in-depth, which is usually expressed in physical terms as multiple barriers to release of radioactive material (e.g. cladding, reactor vessel, containment building), but it is understood that the 'barriers' may consist of active systems or even procedures. As implemented in a reactor design, defense-in-depth is classed in levels of safety. Level 1 includes measures to specify and build a reliable design with significant safety margins that will perform according to the intentions of the designers. Level 2 consists of additional design measures, usually active systems, to protect against unlikely accidental events that may occur during the life of the plant. Level 3 design measures are intended to protect the public in the event of an extremely unlikely accident not foreseen to occur during the plant's life. All of the design measures that make up the first three levels of safety are within the design basis of the plant. Beyond Level 3, and beyond the normal design basis, there are accidents that are not expected to occur in a whole generation of plants, and it is in this class that severe accidents, i.e. accidents involving core melting, are included. Beyond design basis measures to address severe accidents are usually identified as being for prevention of progression into severe accident conditions (prevention of core melting) or for mitigation of severe accident consequences (mitigation of the impact of core melting to protect public health and safety). Because design measures for severe accident prevention and mitigation are beyond the normal design basis, established regulatory guidelines and codes do not provide explicit identification of the design performance requirements for severe accident accommodation. The treatment of severe accidents is one of the key issues of R&D plans for the Gen IV systems in general, and for the Sodium Fast Reactor (SFR) in particular. Despite the lack of an unambiguous definition of safety approach applicable for severe accidents, there is an emerging consensus on the need for their consideration for the design. The US SFR program and Argonne National Laboratory (ANL) in particular have actively studied the potential scenarios and consequences of Hypothetical Core Disruptive Accidents (HCDA) for SFRs with oxide fuel during the Fast Flux Test Facility (FFTF) and Clinch River Breeder Reactor Plant (CRBRP) programs in the 70s and 80s. Later, the focus of the US SFR safety R&D activities shifted to the prevention of all HCDAs through passive safety features of the SFRs with metal fuel in the Integral Fast Reactor (IFR) program, and the study of severe accident consequences was de-emphasized. The goal of this paper is to provide an overview of the current SFR safety approach and the role of severe accidents in Japan and France, in preparation for an expected and more active collaboration in this area between the US, Japan, and France.

  17. Hasanuddinia maxomyos n. gen., n. sp. and Heligmonoides musseri n. sp. (Nematoda: Heligmonellidae) collected from endemic murines of Sulawesi, Indonesia.

    PubMed

    Hasegawa, H; Syafruddin

    1994-10-01

    Two new nematodes belonging to the subfamily Nippostrongylinae (Nematoda: Trichostrongyloidea: Heligmonellidae) are described based on specimens from endemic murines of Sulawesi, Indonesia: Hasanuddinia maxomyos n. gen., n. sp. from Maxomys musschenbroekii and Eropeplus canus, and Heligmonoides musseri n. sp. from M. musschenbroekii, E. canus, and Margaretamys elegans. Hasanuddinia is closest to Rattusstrongylus of Malaysian rats in lacking a carene and in having a lateromedian gradient in the size of the synlophe ridges in the ventral side of the midbody but is distinguished in that the dorsal ray is divided in the distal half. Heligmonoides musseri most resembles H. bulbosus of Maxomys whiteheadi of Malaysia in having a carene supported by slender ridges of which the proximal portion is not thickened but is distinguished in having longer externodorsal rays and longer spicules. The ancestors of the present Sulawesi nematodes seem to have originated on the southeast Asian continent, were introduced to Sulawesi with the dispersal of some murines, and subsequently speciated. PMID:7931913

  18. Haootia quadriformis n. gen., n. sp., interpreted as a muscular cnidarian impression from the Late Ediacaran period (approx. 560 Ma).

    PubMed

    Liu, Alexander G; Matthews, Jack J; Menon, Latha R; McIlroy, Duncan; Brasier, Martin D

    2014-10-22

    Muscle tissue is a fundamentally eumetazoan attribute. The oldest evidence for fossilized muscular tissue before the Early Cambrian has hitherto remained moot, being reliant upon indirect evidence in the form of Late Ediacaran ichnofossils. We here report a candidate muscle-bearing organism, Haootia quadriformis n. gen., n. sp., from approximately 560 Ma strata in Newfoundland, Canada. This taxon exhibits sediment moulds of twisted, superimposed fibrous bundles arranged quadrilaterally, extending into four prominent bifurcating corner branches. Haootia is distinct from all previously published contemporaneous Ediacaran macrofossils in its symmetrically fibrous, rather than frondose, architecture. Its bundled fibres, morphology, and taphonomy compare well with the muscle fibres of fossil and extant Cnidaria, particularly the benthic Staurozoa. Haootia quadriformis thus potentially provides the earliest body fossil evidence for both metazoan musculature, and for Eumetazoa, in the geological record. PMID:25165764

  19. Third-Party Evaluation of Petro Tex Hydrocarbons, LLC, ReGen Lubricating Oil Re-refining Process

    SciTech Connect

    Compere, A L; Griffith, William {Bill} L

    2009-04-01

    This report presents an assessment of market, energy impact, and utility of the PetroTex Hydrocarbons, LLC., ReGen process for re-refining used lubricating oil to produce Group I, II, and III base oils, diesel fuel, and asphalt. PetroTex Hydrocarbons, LLC., has performed extensive pilot scale evaluations, computer simulations, and market studies of this process and is presently evaluating construction of a 23 million gallon per year industrial-scale plant. PetroTex has obtained a 30 acre site in the Texas Industries RailPark in Midlothian Texas. The environmental and civil engineering assessments of the site are completed, and the company has been granted a special use permit from the City of Midlothian and air emissions permits for the Texas Commission on Environmental Quality.

  20. Taxonomic studies on a new marine ciliate, Apocoleps magnus gen. nov., spec. nov. (Ciliophora, Colepidae), isolated from Qingdao, China

    NASA Astrophysics Data System (ADS)

    Chen, Xiangrui; Warren, Alan; Song, Weibo

    2009-12-01

    The morphology and infraciliature of a new marine colepid ciliate, Apocoleps magnus gen. nov., spec. nov., are described based on living observations and silver impregnations. The new genus Apocoleps is characterized by having 8 (vs. 6 in most other related genera) armour tiers, spines at both ends of the cell, 3 adoral organelles and plates with 4 reniform uni-windows. Apocoleps magnus spec. nov. is defined by the following features: body elongated and slightly curved, about 100-120µm× 35-45 µm in vivo; anterior tertiary tier plate with four uni-windows, most secondary and main tier plates with four uni-windows, posterior tertiary tier plate with two uni-windows; left plate margin slightly serrated; on average 23 transverse and 22 longitudinal ciliary rows; one terminal contractile vacuole; marine habitat.

  1. A new genus of Strepsiptera, Rozenia gen. n. (Stylopidae), a parasite of bee genera Acamptopoeum and Calliopsis (Andrenidae, Panurginae, Calliopsini)

    PubMed Central

    Straka, Jakub; J?zová, Katerina; Batelka, Jan

    2014-01-01

    Abstract A new Strepsiptera genus from South America is described, Rozenia gen. n., with three new species: Rozenia calliopsidis sp. n. (type species), Rozenia peruana sp. n. and Rozenia platicephala sp. n. These three new species are parasites of bees belonging to the tribe Calliopsini (Andrenidae, Panurginae). Rozenia calliopsidis sp. n. is a parasite of the bee genus Calliopsis Smith, 1853 and Rozenia peruana sp. n. and Rozenia platicephala sp. n. are parasites of the bee genus Acamptopoeum Cockerell, 1905. Diagnoses and descriptions of female puparia are presented for all three species. Diagnoses and descriptions of first instars (triungulinids) are presented for Rozenia calliopsidis sp. n. and Rozenia platicephala sp. n. The first case of increased number of setae on the body of the first instars and augmentation of chaetotaxy of Strepsiptera are discussed. PMID:25349488

  2. Study of Gryllacridinae (Orthoptera: Stenopelmatidae) from Thailand and
    adjacent countries: the genera Ultragryllacris gen. nov. and Capnogryllacris.

    PubMed

    Gorochov, Andrej V; Dawwrueng, Pattarawich; Artchawakom, Taksin

    2015-01-01

    A new material on the genera Ultragryllacris gen. nov. and Capnogryllacris Karny, 1937 from Thailand, Laos and Cambodia is considered. Five new species and subspecies are described: U. pulchra sp. nov.; U. p. alboclypeata subsp. nov.; C. thaica sp. nov.; C. sakaerat sp. nov.; C. phaeocephala cambodiensis subsp. nov. Capnogryllacris s. l. is divided into two possible subgenera (Capnogryllacris s. str. and Dictyogryllacris Karny, 1937, stat. nov.) as a minimum; the former genera Borneogryllacris Karny, 1937, syn. nov., Marthogryllacris Karny, 1937, syn. nov. and Erythrogryllacris Karny, 1937, syn. nov. are treated as synonyms of the subgenus Capnogryllacris. Previously unknown female for C. khmerica Gorochov, 2003 is described; neotype for C. martha (Griffini, 1914 ), type species of Marthogryllacris, is designated; C. erythrocephala Gorochov, 2003, sp. ressur. and C. e. borealis Gorochov, 2003, stat. ressur. are restored from synonyms of C. martha and from species status, respectively. PMID:26624154

  3. Rhopalomma stefaniae gen. et sp. n., the first ommatid beetle from the Upper Jurassic in Australia (Coleoptera: Archostemata: Ommatidae).

    PubMed

    Ashman, Lauren G; Oberprieler, Rolf G; ?lipi?ski, Adam

    2015-01-01

    The first Upper Jurassic fossil of the family Ommatidae (Coleoptera: Archostemata) from Australia is described and illustrated from a single specimen discovered at the Talbragar Fish Bed. Rhopalomma stefaniae gen. et sp. n. is classified in Ommatidae based on the length and insertion of the antennae, the tuberculate cuticle, the pattern of elytral striae, the complete epipleura and the presence of scutellary strioles. Due to the lack of preservation of crucial characters, Rhopalomma cannot be assigned to a subfamily and is therefore classified as Ommatidae incertae sedis. Rhopalomma fills an important gap in the fossil record of the family, indicating that Ommatidae occurred in Australia from the Lower Jurassic to the present day. Australia is the only place in the world where this family is found in both the fossil record and the living fauna. PMID:26249943

  4. Lachnobacterium bovis gen. nov., sp. nov., a novel bacterium isolated from the rumen and faeces of cattle.

    PubMed

    Whitford, M F; Yanke, L J; Forster, R J; Teather, R M

    2001-11-01

    Phenotypic and phylogenetic analysis was performed on four strains of a previously undescribed Gram-positive, rod-shaped, anaerobic bacterium isolated from the rumen and faeces of cattle. This bacterium fermented glucose primarily to lactic acid along with minor amounts of acetic and butyric acids. The four strains produced a temperature-sensitive bacteriocin-like inhibitory substance. Comparative 16S rRNA gene sequence analysis indicated that the bacterium was a member of the clostridial XIVa cluster of the low-G+C content Gram-positive bacteria. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be assigned to a new genus, Lachnobacterium, as Lachnobacterium bovis gen. nov., sp. nov. The type strain is YZ 87T (= ATCC BAA-151T = DSM 14045T = LRC 5382T). Its G+C content is 33.9 mol %. PMID:11760937

  5. Pseudofornicia gen. n. (Hymenoptera, Braconidae, Microgastrinae), a new Indo-Australian genus and one new species from Vietnam

    PubMed Central

    van Achterberg, Cornelis; Long, Khuat Dang; Chen, Xue-xin; You, Lan-shao

    2015-01-01

    Abstract Pseudofornicia gen. n. (Hymenoptera: Braconidae: Microgastrinae) is described (type species: Pseudofornicia nigrisoma sp. n. from Vietnam) including three Oriental (type species, Pseudofornicia flavoabdominis (He & Chen, 1994), comb. n. and Pseudofornicia vanachterbergi Long, (nom. n. for Fornicia achterbergi Long, 2007; not Fornicia achterbergi Yang & Chen, 2006) and one Australian species (Pseudofornicia commoni (Austin & Dangerfield, 1992), comb. n.). Keys to genera with similar metasomal carapace and to species of the new genus are provided. The new genus shares the curved inner middle tibial spur, the comparatively small head, the median carina of the first metasomal tergite and the metasomal carapace with Fornicia Brullé, 1846, but has the first tergite movably joined to the second tergite and the third tergite 1.1–1.6 × as long as the second tergite medially and is flattened in lateral view. One of the included species is a primary homonym and is renamed in this paper. PMID:26478707

  6. Haootia quadriformis n. gen., n. sp., interpreted as a muscular cnidarian impression from the Late Ediacaran period (approx. 560 Ma)

    PubMed Central

    Liu, Alexander G.; Matthews, Jack J.; Menon, Latha R.; McIlroy, Duncan; Brasier, Martin D.

    2014-01-01

    Muscle tissue is a fundamentally eumetazoan attribute. The oldest evidence for fossilized muscular tissue before the Early Cambrian has hitherto remained moot, being reliant upon indirect evidence in the form of Late Ediacaran ichnofossils. We here report a candidate muscle-bearing organism, Haootia quadriformis n. gen., n. sp., from approximately 560 Ma strata in Newfoundland, Canada. This taxon exhibits sediment moulds of twisted, superimposed fibrous bundles arranged quadrilaterally, extending into four prominent bifurcating corner branches. Haootia is distinct from all previously published contemporaneous Ediacaran macrofossils in its symmetrically fibrous, rather than frondose, architecture. Its bundled fibres, morphology, and taphonomy compare well with the muscle fibres of fossil and extant Cnidaria, particularly the benthic Staurozoa. Haootia quadriformis thus potentially provides the earliest body fossil evidence for both metazoan musculature, and for Eumetazoa, in the geological record. PMID:25165764

  7. Leptohelia flexibilis gen. nov. et sp. nov., a remarkable deep-sea stylasterid (Cnidaria: Hydrozoa: Stylasteridae) from the southwest Pacific.

    PubMed

    Lindner, Alberto; Cairns, Stephen D; Zibrowius, Helmut

    2014-01-01

    Leptohelia flexibilis gen. nov. et sp. nov., the first stylasterid with a combined calcified and non-calcified skeleton, is described from seamounts and the slope off the islands of New Caledonia, in the southwestern Pacific. The new species is distinguished from all other species of the family Stylasteridae by having a non-calcified organic axis, internal to the basal portion of the calcified corallum. The internal axis is flexible and enclosed by a series of up to 10 calcified annuli, allowing passive lateral bending of the colony. Molecular phylogenetic analyses confirm that Leptohelia flexibilis is a stylasterid coral and reveal that the species is closely related to Leptohelia microstylus comb. nov., a southwestern Pacific stylasterid that lacks an internal axis. PMID:25543758

  8. Fukuyoa paulensis gen. et sp. nov., a New Genus for the Globular Species of the Dinoflagellate Gambierdiscus (Dinophyceae)

    PubMed Central

    Gómez, Fernando; Qiu, Dajun; Lopes, Rubens M.; Lin, Senjie

    2015-01-01

    The marine epiphytic dinoflagellate Gambierdiscus is a toxicologically important genus responsible for ciguatera fish poisoning, the principal cause of non-bacterial illness associated with fish consumption. The genus currently contains species exhibiting either globular or anterior-posteriorly compressed morphologies with marked differences in cell shape and plate arrangement. Here we report a third globular, epiphytic and tychoplanktonic species from the coasts of Ubatuba, Brazil. The new species can be distinguished from G. yasumotoi and G. ruetzleri by its broader first apical plate that occupies a larger portion of the epitheca. Accordingly, phylogenetic trees from small subunit (SSU) and large subunit (LSU) ribosomal DNA sequences also showed strongly supported separation of the new species from the G. yasumotoi / G. ruetzleri group albeit with short distance. The molecular phylogenies, which included new sequences of the planktonic species Goniodoma polyedricum, further indicated that the globular species of Gambierdiscus formed a tight clade, clearly separated (with strong bootstrap support) from the clade of lenticular species including the type for Gambierdiscus. The morphological and molecular data in concert support the split of Gambierdiscus sensu lato into two genera. Gambierdiscus sensu stricto should be reserved for the species with lenticular shapes, highly compressed anterioposteriorly, with short-shank fishhook apical pore plate, large 2' plate, low and ascending cingular displacement, and pouch-like sulcal morphology. The new genus name Fukuyoa gen. nov. should be applied to the globular species, slightly laterally compressed, with long-shank fishhook apical pore plate, large 1' plate, greater and descending cingular displacement, and not pouch-like vertically-oriented sulcal morphology. Fukuyoa contains the new species Fukuyoa paulensis gen. et sp. nov., and F. yasumotoi comb. nov. and F. ruetzleri comb. nov. PMID:25831082

  9. Fukuyoa paulensis gen. et sp. nov., a new genus for the globular species of the dinoflagellate Gambierdiscus (Dinophyceae).

    PubMed

    Gómez, Fernando; Qiu, Dajun; Lopes, Rubens M; Lin, Senjie

    2015-01-01

    The marine epiphytic dinoflagellate Gambierdiscus is a toxicologically important genus responsible for ciguatera fish poisoning, the principal cause of non-bacterial illness associated with fish consumption. The genus currently contains species exhibiting either globular or anterior-posteriorly compressed morphologies with marked differences in cell shape and plate arrangement. Here we report a third globular, epiphytic and tychoplanktonic species from the coasts of Ubatuba, Brazil. The new species can be distinguished from G. yasumotoi and G. ruetzleri by its broader first apical plate that occupies a larger portion of the epitheca. Accordingly, phylogenetic trees from small subunit (SSU) and large subunit (LSU) ribosomal DNA sequences also showed strongly supported separation of the new species from the G. yasumotoi/G. ruetzleri group albeit with short distance. The molecular phylogenies, which included new sequences of the planktonic species Goniodoma polyedricum, further indicated that the globular species of Gambierdiscus formed a tight clade, clearly separated (with strong bootstrap support) from the clade of lenticular species including the type for Gambierdiscus. The morphological and molecular data in concert support the split of Gambierdiscus sensu lato into two genera. Gambierdiscus sensu stricto should be reserved for the species with lenticular shapes, highly compressed anterioposteriorly, with short-shank fishhook apical pore plate, large 2' plate, low and ascending cingular displacement, and pouch-like sulcal morphology. The new genus name Fukuyoa gen. nov. should be applied to the globular species, slightly laterally compressed, with long-shank fishhook apical pore plate, large 1' plate, greater and descending cingular displacement, and not pouch-like vertically-oriented sulcal morphology. Fukuyoa contains the new species Fukuyoa paulensis gen. et sp. nov., and F. yasumotoi comb. nov. and F. ruetzleri comb. nov. PMID:25831082

  10. Enhanced/synthetic vision and head-worn display technologies for terminal maneuvering area NextGen operations

    NASA Astrophysics Data System (ADS)

    Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Williams, Steven P.; Bailey, Randall E.; Shelton, Kevin J.; Norman, R. Mike

    2011-06-01

    NASA is researching innovative technologies for the Next Generation Air Transportation System (NextGen) to provide a "Better-Than-Visual" (BTV) capability as adjunct to "Equivalent Visual Operations" (EVO); that is, airport throughputs equivalent to that normally achieved during Visual Flight Rules (VFR) operations rates with equivalent and better safety in all weather and visibility conditions including Instrument Meteorological Conditions (IMC). These new technologies build on proven flight deck systems and leverage synthetic and enhanced vision systems. Two piloted simulation studies were conducted to access the use of a Head-Worn Display (HWD) with head tracking for synthetic and enhanced vision systems concepts. The first experiment evaluated the use a HWD for equivalent visual operations to San Francisco International Airport (airport identifier: KSFO) compared to a visual concept and a head-down display concept. A second experiment evaluated symbology variations under different visibility conditions using a HWD during taxi operations at Chicago O'Hare airport (airport identifier: KORD). Two experiments were conducted, one in a simulated San Francisco airport (KSFO) approach operation and the other, in simulated Chicago O'Hare surface operations, evaluating enhanced/synthetic vision and head-worn display technologies for NextGen operations. While flying a closely-spaced parallel approach to KSFO, pilots rated the HWD, under low-visibility conditions, equivalent to the out-the-window condition, under unlimited visibility, in terms of situational awareness (SA) and mental workload compared to a head-down enhanced vision system. There were no differences between the 3 display concepts in terms of traffic spacing and distance and the pilot decision-making to land or go-around. For the KORD experiment, the visibility condition was not a factor in pilot's rating of clutter effects from symbology. Several concepts for enhanced implementations of an unlimited field-of-regard BTV concept for low-visibility surface operations were determined to be equivalent in pilot ratings of efficacy and usability.

  11. Enhanced/Synthetic Vision and Head-Worn Display Technologies for Terminal Maneuvering Area NextGen Operations

    NASA Technical Reports Server (NTRS)

    Arthur, Jarvis J., III; Prinzell, Lawrence J.; Williams, Steven P.; Bailey, Randall E.; Shelton, Kevin J.; Norman, R. Mike

    2011-01-01

    NASA is researching innovative technologies for the Next Generation Air Transportation System (NextGen) to provide a "Better-Than-Visual" (BTV) capability as adjunct to "Equivalent Visual Operations" (EVO); that is, airport throughputs equivalent to that normally achieved during Visual Flight Rules (VFR) operations rates with equivalent and better safety in all weather and visibility conditions including Instrument Meteorological Conditions (IMC). These new technologies build on proven flight deck systems and leverage synthetic and enhanced vision systems. Two piloted simulation studies were conducted to access the use of a Head-Worn Display (HWD) with head tracking for synthetic and enhanced vision systems concepts. The first experiment evaluated the use a HWD for equivalent visual operations to San Francisco International Airport (airport identifier: KSFO) compared to a visual concept and a head-down display concept. A second experiment evaluated symbology variations under different visibility conditions using a HWD during taxi operations at Chicago O'Hare airport (airport identifier: KORD). Two experiments were conducted, one in a simulated San Francisco airport (KSFO) approach operation and the other, in simulated Chicago O'Hare surface operations, evaluating enhanced/synthetic vision and head-worn display technologies for NextGen operations. While flying a closely-spaced parallel approach to KSFO, pilots rated the HWD, under low-visibility conditions, equivalent to the out-the-window condition, under unlimited visibility, in terms of situational awareness (SA) and mental workload compared to a head-down enhanced vision system. There were no differences between the 3 display concepts in terms of traffic spacing and distance and the pilot decision-making to land or go-around. For the KORD experiment, the visibility condition was not a factor in pilot's rating of clutter effects from symbology. Several concepts for enhanced implementations of an unlimited field-of-regard BTV concept for low-visibility surface operations were determined to be equivalent in pilot ratings of efficacy and usability.

  12. Comparison of Fracture Gradient Methods for the FutureGen 2.0 Carbon Storage Site, Ill., USA.

    NASA Astrophysics Data System (ADS)

    Appriou, D.; Spane, F.; Wurstner White, S.; Kelley, M. E.; Sullivan, E. C.; Bonneville, A.; Gilmore, T. J.

    2014-12-01

    As part of a first-of-its-kind carbon dioxide storage project, FutureGen Industrial Alliance is planning to inject 1.1 MMt/yr of supercritical CO2 over a 20-year period within a 1240 m deep saline aquifer (Mount Simon Sandstone) located in Morgan County, Illinois, USA. Numerous aspects of the design and operational activities of the CO2 storage site are dependent on the geomechanical properties of the targeted reservoir zone, as well as of the overlying confining zone and the underlying crystalline Precambrian basement. Detailed determination of the state-of-stress within the subsurface is of paramount importance in successfully designing well drilling/completion aspects, as well as assessing the risk of induced seismicity and the potential for creating and/or reopening pre-existing fractures; all of which help ensure the safe long-term storage of injected CO2. The quantitative determination of the subsurface fracture gradient is one of the key geomechanical parameters for the site injection design and operational limits (e.g., maximum safe injection pressure). A characterization well drilled in 2011 provides subsurface geomechanical characterization information for the FutureGen 2.0 site, and includes: 1) continuous elastic properties inferred from sonic/acoustic wireline logs 2) discrete depth geomechanical laboratory core measurements and 3) results obtained from hydraulic fracturing tests of selected borehole/depth-intervals. In this paper, the precise fracture gradients derived from borehole geomechanical test results are compared with semi-empirical, fracture gradient calculation/relationships based on elastic property wireline surveys and laboratory geomechanical core test results. Implications for using various fracture-gradients obtained from the different methods are assessed using PNNL's subsurface multiphase flow and transport simulator STOMP-CO2. The implications for operational activities at the site (based on using different fracture gradients) are also discussed.

  13. FutureGen 2.0 Monitoring Program: An Overview of the Monitoring Approach and Technologies Selected for Implementation

    DOE PAGESBeta

    Vermeul, Vince R.; Strickland, Chris E.; Thorne, Paul D.; Bjornstad, Bruce N.; Mackley, Rob D.; Kelly, Mark E.; Sullivan, Charlotte; Williams, Mark D.; Amonette, James E.; Downs, Janelle L.; et al

    2014-12-31

    The FutureGen 2.0 Project will design and build a first-of-its-kind, near-zero emissions coal-fueled power plant with carbon capture and storage (CCS). To assess storage site performance and meet the regulatory requirements of the Class VI Underground Injection Control (UIC) Program for CO2 Geologic Sequestration, the FutureGen 2.0 project will implement a suite of monitoring technologies designed to 1) evaluate CO2 mass balance and 2) detect any unforeseen loss in CO2 containment. The monitoring program will include direct monitoring of the injection stream and reservoir, and early-leak-detection monitoring directly above the primary confining zone. It will also implement an adaptive monitoringmore »strategy whereby monitoring results are continually evaluated and the monitoring network is modified as required, including the option to drill additional wells in out-years. Wells will be monitored for changes in CO2 concentration and formation pressure, and other geochemical/isotopic signatures that provide indication of CO2 or brine leakage. Indirect geophysical monitoring technologies that were selected for implementation include passive seismic, integrated surface deformation, time-lapse gravity, and pulsed neutron capture logging. Near-surface monitoring approaches that have been initiated include surficial aquifer and surface- water monitoring, soil-gas monitoring, atmospheric monitoring, and hyperspectral data acquisition for assessment of vegetation conditions. Initially, only the collection of baseline data sets is planned; the need for additional near- surface monitoring will be continually evaluated throughout the design and operational phases of the project, and selected approaches may be reinstituted if conditions warrant. Given the current conceptual understanding of the subsurface environment, early and appreciable impacts to near-surface environments are not expected.« less

  14. Evaluating the Suitability for CO2 Storage at the FutureGen 2.0 Site, Morgan County, Illinois, USA

    SciTech Connect

    Bonneville, Alain; Gilmore, Tyler J.; Sullivan, E. C.; Vermeul, Vincent R.; Kelley, Mark E.; White, Signe K.; Appriou, Delphine; Bjornstad, Bruce N.; Gerst, Jacqueline L.; Gupta, Neeraj; Horner, Jacob A.; McNeil, Caitlin; Moody, Mark A.; Rike, William M.; Spane, Frank A.; Thorne, Paul D.; Zeller, Evan R.; Zhang, Z. F.; Hoffman, Jeffrey; Humphreys, Kenneth K.

    2013-08-05

    FutureGen 2.0 site will be the first near-zero emission power plant with fully integrated long-term storage in a deep, non-potable saline aquifer in the United States. The proposed FutureGen 2.0 CO2 storage site is located in northeast Morgan County, Illinois, U.S.A., forty-eight kilometres from the Meredosia Energy Center where a large-scale oxy-combustion demonstration will be conducted. The demonstration will involve > 90% carbon capture, which will produce more than one million metric tons (MMT) of CO2 per year. The CO2 will be compressed at the power plant and transported via pipeline to the storage site. To examine CO2 storage potential of the site, a 1,467m characterization well (FGA#1) was completed in December 2011. The target reservoir for CO2 storage is the Mt. Simon Sandstone and Elmhurst Sandstone Member of the lower Eau Claire Formation for a combined thickness of 176 m. Confining beds of the overlying Lombard and Proviso Members (upper Eau Claire Formation) reach a thickness of 126 m. Characterization of the target injection zone and the overlying confining zone was based on wellbore data, cores, and geophysical logs, along with surface geophysical (2-D seismic profiles, magnetic and gravity), and structural data collected during the initial stage of the project . Based on this geological model, 3D simulations of CO2 injection and redistribution were conducted using STOMP-CO2, a multiphase flow and transport simulator. After this characterization stage, it appears that the injection site is a suitable geologic system for CO2 sequestration and that the injection zone is sufficient to receive up to 33 MMT of CO2 at a rate of 1.1 MMT/yr. GHGT-11 conference

  15. The dismantling of Calliobothrium (Cestoda: Tetraphyllidea) with erection of Symcallio n. gen. and description of two new species.

    PubMed

    Bernot, James P; Caira, Janine N; Pickering, Maria

    2015-04-01

    This paper aims to resolve the dual composition of the triakid shark-hosted tetraphyllidean genus Calliobothrium--an issue that has been recognized for over a decade. As it stands, this genus includes a number of large species with laciniate proglottids, most of which bear 3 suckers at the anterior margin of each bothridium, but it also includes a number of species that lack proglottid laciniations and bear only a single sucker per bothridium, most of which are relatively small. Discovery of 2 new species, 1 of each form, parasitizing the whitespot smoothhound shark, Mustelus palumbes, off South Africa, prompted the first molecular analysis of the genus. Bayesian inference and maximum likelihood analyses of 28S rDNA (D1-D3) sequence data generated for specimens of both new species as well as of 2 known species of the laciniate form (Calliobothrium australis and Calliobothrium cf. verticillatum) and 3 known species of the non-laciniate form (Calliobothrium violae, Calliobothrium riseri, and Calliobothrium barbarae) confirmed the reciprocal monophyly of the 2 clades, supporting establishment of a new genus. Because the type of Calliobothrium, C. verticillatum, is of the laciniate form, Symcallio n. gen., with Symcallio peteri n. gen., n. sp., from M. palumbes described as its type, is established to house members of the non-laciniate clade. The 11 described species consistent with this form are transferred to the new genus. A new species of the laciniate clade, Calliobothrium euzeti n. sp., is described from M. palumbes, and a revised diagnosis of Calliobothrium is presented. PMID:25506725

  16. FutureGen 2.0 Monitoring Program: An Overview of the Monitoring Approach and Technologies Selected for Implementation

    SciTech Connect

    Vermeul, Vince R.; Strickland, Chris E.; Thorne, Paul D.; Bjornstad, Bruce N.; Mackley, Rob D.; Kelly, Mark E.; Sullivan, Charlotte; Williams, Mark D.; Amonette, James E.; Downs, Janelle L.; Fritz, Brad G.; Szecsody, Jim E.; Bonneville, Alain; Gilmore, Tyler J.

    2014-12-31

    The FutureGen 2.0 Project will design and build a first-of-its-kind, near-zero emissions coal-fueled power plant with carbon capture and storage (CCS). To assess storage site performance and meet the regulatory requirements of the Class VI Underground Injection Control (UIC) Program for CO2 Geologic Sequestration, the FutureGen 2.0 project will implement a suite of monitoring technologies designed to 1) evaluate CO2 mass balance and 2) detect any unforeseen loss in CO2 containment. The monitoring program will include direct monitoring of the injection stream and reservoir, and early-leak-detection monitoring directly above the primary confining zone. It will also implement an adaptive monitoring strategy whereby monitoring results are continually evaluated and the monitoring network is modified as required, including the option to drill additional wells in out-years. Wells will be monitored for changes in CO2 concentration and formation pressure, and other geochemical/isotopic signatures that provide indication of CO2 or brine leakage. Indirect geophysical monitoring technologies that were selected for implementation include passive seismic, integrated surface deformation, time-lapse gravity, and pulsed neutron capture logging. Near-surface monitoring approaches that have been initiated include surficial aquifer and surface- water monitoring, soil-gas monitoring, atmospheric monitoring, and hyperspectral data acquisition for assessment of vegetation conditions. Initially, only the collection of baseline data sets is planned; the need for additional near- surface monitoring will be continually evaluated throughout the design and operational phases of the project, and selected approaches may be reinstituted if conditions warrant. Given the current conceptual understanding of the subsurface environment, early and appreciable impacts to near-surface environments are not expected.

  17. Boltimys broomi gen. nov., sp. nov. (Rodentia, Mammalia), nouveau Muridae d'affinité incertaine du Pliocène inférieur d'Afrique du Sud

    NASA Astrophysics Data System (ADS)

    Sénégas, Frank; Michaux, Jacques

    2000-04-01

    Boltimys broomi gen. nov., sp. nov., a Muridae of uncertain affinity in the Early Pliocene of South Africa. Boltimys broomi gen. nov., sp. nov. is reported from the Early Pliocene fauna of Waypoint 160, a fossiliferous locality in the area of Bolt's Farm (Province of Gauteng) near Krugersdorp in South Africa. The occlusal surface of the jugal teeth is characterized by a basin-shaped aspect due to the coalescence of the cusps which make the lobes of the molars. An accessory inner cusp is present on the first and second upper molars. A faint longitudinal crest is present only in the first lower molar. The new rodent is tentatively referred to the subfamily Myocricetodontinae.

  18. A new genus of oak gallwasp, Coffeikokkos Pujade-Villar & Melika, gen. n., with a description of a new species from Costa Rica (Hymenoptera, Cynipidae)

    PubMed Central

    Pujade-Villar, Juli; Hanson, Paul; Melika, George

    2012-01-01

    Abstract A new genus of oak gallwasp, Coffeikokkos Pujade-Villar & Melika, gen. n., is described from Costa Rica. Diagnostic characters and generic limits of the new genus are discussed in detail. The new genus includes Coffeikokkos copeyensis Pujade-Villar & Melika, sp. n., which induces galls on stems of Quercus bumelioides, an endemic oak to Costa Rica, Honduras and Panama. The new species and galls are described and illustrated. PMID:22423188

  19. The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access.

    PubMed

    Goda, Hideki; Sasaki, Eriko; Akiyama, Kenji; Maruyama-Nakashita, Akiko; Nakabayashi, Kazumi; Li, Weiqiang; Ogawa, Mikihiro; Yamauchi, Yukika; Preston, Jeremy; Aoki, Ko; Kiba, Takatoshi; Takatsuto, Suguru; Fujioka, Shozo; Asami, Tadao; Nakano, Takeshi; Kato, Hisashi; Mizuno, Takeshi; Sakakibara, Hitoshi; Yamaguchi, Shinjiro; Nambara, Eiji; Kamiya, Yuji; Takahashi, Hideki; Hirai, Masami Yokota; Sakurai, Tetsuya; Shinozaki, Kazuo; Saito, Kazuki; Yoshida, Shigeo; Shimada, Yukihisa

    2008-08-01

    We analyzed global gene expression in Arabidopsis in response to various hormones and in related experiments as part of the AtGenExpress project. The experimental agents included seven basic phytohormones (auxin, cytokinin, gibberellin, brassinosteroid, abscisic acid, jasmonate and ethylene) and their inhibitors. In addition, gene expression was investigated in hormone-related mutants and during seed germination and sulfate starvation. Hormone-inducible genes were identified from the hormone response data. The effects of each hormone and the relevance of the gene lists were verified by comparing expression profiles for the hormone treatments and related experiments using Pearson's correlation coefficient. This approach was also used to analyze the relationships among expression profiles for hormone responses and those included in the AtGenExpress stress-response data set. The expected correlations were observed, indicating that this approach is useful to monitor the hormonal status in the stress-related samples. Global interactions among hormones-inducible genes were analyzed in a pairwise fashion, and several known and novel hormone interactions were detected. Genome-wide transcriptional gene-to-gene correlations, analyzed by hierarchical cluster analysis (HCA), indicated that our data set is useful for identification of clusters of co-expressed genes, and to predict the functions of unknown genes, even if a gene's function is not directly related to the experiments included in AtGenExpress. Our data are available online from AtGenExpressJapan; the results of genome-wide HCA are available from PRIMe. The data set presented here will be a versatile resource for future hormone studies, and constitutes a reference for genome-wide gene expression in Arabidopsis. PMID:18419781

  20. A new African soft scale genus, Pseudocribrolecanium gen. nov. (Hemiptera: Coccoidea: Coccidae), erected for two species, including the citrus pest P. andersoni (Newstead) comb. nov

    PubMed Central

    Kondo, Takumasa

    2006-01-01

    A new African genus of soft scale insects, Pseudocribrolecanium gen. nov. is erected to accommodate Akermes colae Green & Laing and Cribrolecanium andersoni (Newstead). The adult females and first-instar nymphs of the two species are redescribed and illustrated. Taxonomic keys to separate the adult females and first-instar nymphs are provided. The affinity of Pseudocribrolecanium with the tribe Paralecaniini in the subfamily Coccinae is discussed. PMID:19537997

  1. AtGEN1 and AtSEND1, Two Paralogs in Arabidopsis, Possess Holliday Junction Resolvase Activity1[W][OPEN

    PubMed Central

    Bauknecht, Markus; Kobbe, Daniela

    2014-01-01

    Holliday junctions (HJs) are physical links between homologous DNA molecules that arise as central intermediary structures during homologous recombination and repair in meiotic and somatic cells. It is necessary for these structures to be resolved to ensure correct chromosome segregation and other functions. In eukaryotes, including plants, homologs of a gene called XPG-like endonuclease1 (GEN1) have been identified that process HJs in a manner analogous to the HJ resolvases of phages, archaea, and bacteria. Here, we report that Arabidopsis (Arabidopsis thaliana), a eukaryotic organism, has two functional GEN1 homologs instead of one. Like all known eukaryotic resolvases, AtGEN1 and Arabidopsis single-strand DNA endonuclease1 both belong to class IV of the Rad2/XPG family of nucleases. Their resolvase activity shares the characteristics of the Escherichia coli radiation and UV sensitive C paradigm for resolvases, which involves resolving HJs by symmetrically oriented incisions in two opposing strands. This leads to ligatable products without the need for further processing. The observation that the sequence context influences the cleavage by the enzymes can be interpreted as a hint for the existence of sequence specificity. The two Arabidopsis paralogs differ in their preferred sequences. The precise cleavage positions observed for the resolution of mobile nicked HJs suggest that these cleavage positions are determined by both the substrate structure and the sequence context at the junction point. PMID:25037209

  2. The Columbus Knee System: 4-Year Results of a New Deep Flexion Design Compared to the NexGen Full Flex Implant

    PubMed Central

    Goebel, D.; Schultz, W.

    2012-01-01

    The Columbus knee system is designed as a standard knee implant to allow high flexion without additional bone resection. Between August, 2004 and March, 2010 we performed 109 total knee arthroplasties of the Columbus knee system in 101 consecutive patients suffering from primary arthrosis of the knee. Mean age was 72.4 years in women and 70.3 years in men. Mean followup was 47.3 months. The 4-year results of a group of patients who received the NexGen Full Flex implant operated by the same surgeon were used for comparison. Mean total knee score was Columbus: 175.6 and NexGen Flex: 183.4; P = 0.037. Mean operation time was 53?min for Columbus and 66?min for NexGen Flex; P < 0.001. With new streamlined instruments operative time became 60?min for the Columbus; P > 0.05. Radiological assessment showed no signs of loosening for both groups. Therefore, the Columbus knee system can be recommended for flexion angles up to 140°. PMID:22496976

  3. Results of Total Knee Arthroplasty with NexGen LPS-flex Implant Using Navigation System (Brain Lab): Results with a 5-year Follow-up

    PubMed Central

    Kang, Chul Hyung; Lee, Kyung Jae; Cho, Chul Hyun; Lee, Si Wook; Shin, Hong Kwan; Lee, Young Kook; Bae, Ji Suk

    2012-01-01

    Purpose To evaluate the clinical and radiological results of patients that underwent total knee arthroplasty (TKA) with a NexGen LPS-Flex implant using a Navigation system (Brain Lab). Materials and Methods Between January 2001 and December 2005, 55 knees in 46 patients which used the NexGen LPS-Flex implant with a Navigation system (Brain Lab) for primary TKA were clinically and radiologically evaluated after a minimum follow-up of 5 years. Evaluation included preoperative and postoperative range of motion (ROM), Knee Society Score (KSS), tibio-femoral angle and postoperative complications. Results Knee ROM was increased from 118.9° preoperatively to 126.9° at the last follow up. In addition, the preoperative flexion contracture improved from 6.5° to 1.8° postoperatively. The mean KSS and functional score were improved from 59.8 and 51.2 to postoperative scores of 86.4 and 85.2 respectively. The rate of appearance of radiolucency in X-ray was 21.8%. One case of superficial skin infection and one case of aseptic loosening were noted as complications but, did not require a revision surgery. Conclusions TKA with NexGen LPS-Flex implant using Navigation system (Brain Lab) showed satisfactory improvement in pain and function, but more long term follow up will be needed to complete verification. PMID:23269958

  4. Description of Fimbriimonas ginsengisoli gen. nov., sp. nov. within the Fimbriimonadia class nov., of the phylum Armatimonadetes.

    PubMed

    Im, Wan-Taek; Hu, Zi-Ye; Kim, Kyoung-Ho; Rhee, Sung-Keun; Meng, Han; Lee, Sung-Taik; Quan, Zhe-Xue

    2012-08-01

    Strain Gsoil 348(T) was isolated from a ginseng field soil sample by selecting micro-colonies from one-fifth strength modified R2A agar medium after a long incubation period. 16S rRNA gene sequence analysis indicated that the strain is related to members of the phylum Armatimonadetes (formerly called candidate phylum OP10). Strain Gsoil 348(T) is mesophilic, strictly aerobic, non-motile and rod-shaped. It only grows in low nutrient media. The major respiratory quinones are menaquinones MK-11 and MK-10, and the main fatty acids are iso-C(15:0), iso-C(17:0), C(16:0) and C(16:1) ?11c. The G+C content is 61.4 mol%. The 16S rRNA gene sequences in public databases belonging to the phylum Armatimonadetes were clustered here into 6 groups. Five of these groups constituted a coherent cluster distinct from the sequences of other phyla in phylogenetic trees that were constructed using multiple-outgroup sequences from 49 different phyla. On the basis of polyphasic taxonomic analyses, it is proposed that strain Gsoil 348(T) (= KACC 14959(T) = JCM 17079(T)) should be placed in Fimbriimonas ginsengisoli gen. nov., sp. nov., as the cultured representative of the Fimbriimonadia class. nov., corresponding with Group 4 of the phylum Armatimonadetes. PMID:22527625

  5. Thiobacimonas profunda gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from deep-sea water.

    PubMed

    Li, Shuhui; Tang, Kai; Liu, Keshao; Jiao, Nianzhi

    2015-02-01

    A bacterial strain, JLT2016(T), was isolated from a sample of South-eastern Pacific deep-sea water. Cells were Gram-stain-negative, aerobic, devoid of flagella, motile by gliding and rod-shaped. Colonies were mucoid and cream. Growth occurred at 1.0-11.0 % (w/v) NaCl, 10-40 °C and pH 4.0-9.0. The major fatty acids were summed feature 8 (C18 : 1?7c and/or C18 : 1?6c) (60.5 %), C19 : 0 cyclo ?8c (10.9 %) and C16 : 0 (9.0 %). The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two sphingoglycolipids. The DNA G+C content was 67.1 mol%. The closest relative of strain JLT2016(T) was Salipiger mucosus A3(T) (96.7 % 16S rRNA gene sequence similarity). The results of phylogenetic analyses with different treeing algorithms indicated that this strain belonged to the Roseobacter clade in the order Rhodobacterales. Based on polyphasic analysis, strain JLT2016(T) is considered to represent a novel genus and species, for which the name Thiobacimonas profunda gen. nov., sp. nov. is proposed. The type strain is JLT2016(T) (?= LMG 27365(T)?= CGMCC 1.12377(T)). PMID:25355706

  6. Arenitalea lutea gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from intertidal sand.

    PubMed

    Zhang, Xi-Ying; Liu, Ang; Liu, Chang; Li, Hai; Li, Guo-Wei; Xu, Zhong; Chen, Xiu-Lan; Zhou, Bai-Cheng; Zhang, Yu-Zhong

    2013-08-01

    A yellow, rod-shaped, Gram-negative, facultatively aerobic, gliding bacterium, designed strain P7-3-5(T), was isolated from intertidal sand of the Yellow Sea, China. Analysis of 16S rRNA gene sequences revealed that strain P7-3-5(T) formed a distinct lineage within the family Flavobacteriaceae, sharing 94.2-96.9 % sequence similarity with type strains of species of the most closely related genera, including Hyunsoonleella, Jejuia, Marinivirga and Algibacter. The strain grew at 4-40 °C and with 0.5-5.0 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed gelatin and DNA. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and anteiso-C15 : 0 and the major respiratory quinone was MK-6. Polar lipids included phosphatidylethanolamine (PE), three unidentified aminolipids (AL1-3) and four unidentified lipids (L1-4). The genomic DNA G+C content of strain P7-3-5(T) was 32.1 mol%. Data from this polyphasic study suggest that strain P7-3-5(T) represents a novel species in a new genus in the family Flavobacteriaceae, for which the name Arenitalea lutea gen. nov., sp. nov. is proposed. The type strain of Arenitalea lutea is P7-3-5(T) ( = CGMCC 1.12213(T) = KACC 16457(T)). PMID:23315415

  7. Morphology and ontogenesis of Psilotrichides hawaiiensis nov. gen., nov. spec. and molecular phylogeny of the Psilotrichidae (Ciliophora, Hypotrichia).

    PubMed

    Heber, Domingo; Stoeck, Thorsten; Foissner, Wilhelm

    2014-01-01

    The Psilotrichidae are a family of middle-sized hypotrichs with unique morphological and ontogenetic features (e.g. the oral primordium develops in a deep pouch) that, however, did not provide a definite phylogenetic signal. Thus, we studied the 18S rRNA gene of Urospinula succisa (Müller 1786) Esteban et al., 2001 as well as the morphology and ontogenesis of Psilotrichides hawaiiensis, a new genus and species from an ephemeral swamp on Oahu Island, Hawaii. The molecular data classify the psilotrichids into the oxytrichids but without clear branching position. A brief revision, using the structure of the oral apparatus, the location of the contractile vacuole, and three ontogenetic features, showed four distinct genera: Psilotricha Stein, 1859; Urospinula Corliss, 1960; Hemiholosticha Gelei, 1954; and Psilotrichides nov. gen., which differs from the confamilials mainly by the obliquely oriented buccal cavity and the shape of the undulating membranes as well as by a distinct ridge along the right buccal margin. The pyriform species, P. hawaiiensis, is about 65 × 45 ?m in size and is easily recognized by the table tennis racket-shaped appearance due to the elongated last cirrus of the left marginal row. Refined diagnoses are provided for the family Psilotrichidae Bütschli, 1889 and the genera contained. PMID:24498929

  8. The eGenVar data management system--cataloguing and sharing sensitive data and metadata for the life sciences.

    PubMed

    Razick, Sabry; Mo?nik, Rok; Thomas, Laurent F; Ryeng, Einar; Drabløs, Finn; Sætrom, Pål

    2014-01-01

    Systematic data management and controlled data sharing aim at increasing reproducibility, reducing redundancy in work, and providing a way to efficiently locate complementing or contradicting information. One method of achieving this is collecting data in a central repository or in a location that is part of a federated system and providing interfaces to the data. However, certain data, such as data from biobanks or clinical studies, may, for legal and privacy reasons, often not be stored in public repositories. Instead, we describe a metadata cataloguing system and a software suite for reporting the presence of data from the life sciences domain. The system stores three types of metadata: file information, file provenance and data lineage, and content descriptions. Our software suite includes both graphical and command line interfaces that allow users to report and tag files with these different metadata types. Importantly, the files remain in their original locations with their existing access-control mechanisms in place, while our system provides descriptions of their contents and relationships. Our system and software suite thereby provide a common framework for cataloguing and sharing both public and private data. Database URL: http://bigr.medisin.ntnu.no/data/eGenVar/. PMID:24682735

  9. Isolation and characterization of Keratinibaculum paraultunense gen. nov., sp. nov., a novel thermophilic, anaerobic bacterium with keratinolytic activity.

    PubMed

    Huang, Yan; Sun, Yingjie; Ma, Shichun; Chen, Lu; Zhang, Hui; Deng, Yu

    2013-08-01

    A novel thermophilic, anaerobic, keratinolytic bacterium designated KD-1 was isolated from grassy marshland. Strain KD-1 was a spore-forming rod with a Gram-positive type cell wall, but stained Gram-negative. The temperature, pH, and NaCl concentration range necessary for growth was 30-65 °C (optimum 55 °C), 6.0-10.5 (optimum 8.0-8.5), and 0-6% (optimum 0.2%) (w/v), respectively. Strain KD-1 possessed extracellular keratinase, and the optimum activity of the crude enzyme was pH 8.5 and 70 °C. The enzyme was identified as a thermostable serine-type protease. The strain was sensitive to rifampin, chloramphenicol, kanamycin, and tetracycline and was resistant to erythromycin, neomycin, penicillin, and streptomycin. The main cellular fatty acid was predominantly C15:0 iso (64%), and the G+C content was 28 mol%. Morphological and physiological characterization, together with phylogenetic analysis based on 16S rRNA gene sequencing identified KD-1 as a new species of a novel genus of Clostridiaceae with 95.3%, 93.8% 16S rRNA gene sequence similarity to Clostridium ultunense BS(T) (DSM 10521(T)) and Tepidimicrobium xylanilyticum PML14(T) (= JCM 15035(T)), respectively. We propose the name Keratinibaculum paraultunense gen. nov., sp. nov., with KD-1 (=JCM 18769(T) =DSM 26752(T)) as the type strain. PMID:23710623

  10. Coralslurrinella hongkonensis gen. nov., sp. nov., a novel bacterium in the family Psychromonadaceae, isolated from the coral Platygyra carnosus.

    PubMed

    Li, Yanxia; Chan, Yuki; Fu, Yingnan; Zhang, Rui; Chiu, Jill M Y

    2013-12-01

    A novel bacterial strain, JLT2006T, was isolated from the scleractinian coral Platygyra carnosus, located in Hong Kong, China. Cells of this strain were Gram-negative, rod-shaped or oval-shaped and motile by the means of polar flagella. They formed faint-yellow, round colonies on marine agar medium. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that the strain JLT2006T belonged to the class Gammaproteobacteria and was most closely related to Alteromonas-like bacteria of the genera Psychromonas, Pseudoalteromonas, Moritella, Shewanella and Ferrimonas, with less than 93 % sequence similarity. The predominant fatty acids were identified as C18:1x7c/C18:1x6c (23.0 %), C16:1x7c/C16:1x6c (18.2 %) and C16:0 (16.4 %). The quinone was menaquinone-7 (100 %). The polar lipids were determined to be phosphatidylglycerol, phosphatidylethanolamine, phospholipid, glycolipid and lipid. The genomic DNA G?C content was 40.3 mol%. Based on the 16S rRNA gene sequence as well as the physiological and biochemical features that separate the strain JLT2006T from other recognized bacteria, a novel species of a new genus with the name Coralslurrinella hongkonensis gen. nov., sp. nov. is proposed. The type strain is JLT2006T (=JCM 18796T = CGMCC 1.10992T). PMID:24022396

  11. Ultrastructure and LSU rDNA-based phylogeny of Peridinium lomnickii and description of Chimonodinium gen. nov. (Dinophyceae).

    PubMed

    Craveiro, Sandra C; Calado, António J; Daugbjerg, Niels; Hansen, Gert; Moestrup, Øjvind

    2011-10-01

    Several populations of Peridinium lomnickii were examined by SEM and serial section TEM. Comparison with typical Peridinium, Peridiniopsis, Palatinus and Scrippsiella species revealed significant structural differences, congruent with phylogenetic hypotheses derived from partial LSU rDNA sequences. Chimonodinium gen. nov. is described as a new genus of peridinioids, characterized by the Kofoidian plate formula Po, cp, x, 4', 3a, 7'', 6c, 5s, 5''', 2'''', the absence of pyrenoids, the presence of a microtubular basket with four or five overlapping rows of microtubules associated with a small peduncle, a pusular system with well-defined pusular tubes connected to the flagellar canals, and the production of non-calcareous cysts. Serial section examination of Scrippsiella trochoidea, here taken to represent typical Scrippsiella characters, revealed no peduncle and no associated microtubular strands. The molecular phylogeny placed C. lomnickii comb. nov. as a sister group to a clade composed of Thoracosphaera and the pfiesteriaceans. Whereas the lack of information on fine structure of the swimming stage of Thoracosphaera leaves its affinities unexplained, C. lomnickii shares with the pfiesteriaceans the presence of a microtubular basket and the unusual connection between two plates on the left side of the sulcus, involving extra-cytoplasmic fibres. PMID:21621455

  12. Ezakiella peruensis gen. nov., sp. nov. isolated from human fecal sample from a coastal traditional community in Peru.

    PubMed

    Patel, Nisha B; Tito, Raul Y; Obregón-Tito, Alexandra J; O'Neal, Lindsey; Trujillo-Villaroel, Omar; Marin-Reyes, Luis; Troncoso-Corzo, Luzmila; Guija-Poma, Emilio; Hamada, Moriyuki; Uchino, Yoshihito; Lewis, Cecil M; Lawson, Paul A

    2015-04-01

    A novel Gram-stain positive, non-motile, non-sporeforming coccus-shaped, obligately anaerobic bacterium was isolated from a fecal sample of an individual residing in a traditional Peruvian community. The organism was characterized using biochemical, chemotaxonomic and phylogenetic methods. Comparative 16S rRNA gene sequence analyses and phenotypic characteristics demonstrated that the organism was biochemically and phenotypically related, but distinct, from a group of organisms referred to as the Gram-stain positive anaerobic cocci (GPAC). The major cellular fatty acids of the novel isolate were determined to be C16:0 (18.3%), C18:1?9c (39.8%), C18:2?6,9c/C18:0 ANTE (13.2%). Fermentation end products from PYG are acetate and formate. Cell-wall peptidoglycan was found to be A4? (L-Lys-L-Ala-L-Glu) and the G + C content was determined to be 38.4 mol%. Based on the phenotypic, chemotaxonomic, and phylogenetic results, Ezakiella peruensis gen. nov., sp. nov., is now proposed. The type strain is M6.X2(T) (DSM 27367(T) = NBRC 109957 (T) = CCUG 64571(T)). PMID:25481562

  13. Suigetsumonas clinomigrationis gen. et sp. nov., a Novel Facultative Anaerobic Nanoflagellate Isolated from the Meromictic Lake Suigetsu, Japan.

    PubMed

    Okamura, Takahiko; Kondo, Ryuji

    2015-09-01

    A novel facultative anaerobic bacterivorous nanoflagellate was isolated from the water just below the permanent oxic-anoxic interface of the meromictic Lake Suigetsu, Japan. We characterized the isolate using light and transmission electron microscopy and molecular phylogenetic analyses inferred from 18S rDNA sequences. The phylogenetic analyses showed that the isolate belonged to class Placididea (stramenopiles). The isolate showed key ultrastructural features of the Placididea, such as flagellar hairs with two unequal terminal filaments, microtubular root 2 changing in shape from an arced to an acute-angled shape, and a lack of an x-fiber in root 2. However, the isolate had a single helix in the flagellar transition region, which is a double helix in the two known placidid nanoflagellates Placidia cafeteriopsis and Wobblia lunata. Moreover, the isolate had different intracellular features compared with these two genera, such as the arrangement of basal bodies, the components of the flagellar apparatus, the number of mitochondria, and the absence (or presence) of paranuclear bodies. The 18S rDNA sequence was also phylogenetically distant from the clades of the known Placididae W. lunata and P. cafeteriopsis. Consequently, the newly isolated nanoflagellate was described as Suigetsumonas clinomigrationis gen. et sp. nov. PMID:26202992

  14. ‘Candidatus Megaira polyxenophila’ gen. nov., sp. nov.: Considerations on Evolutionary History, Host Range and Shift of Early Divergent Rickettsiae

    PubMed Central

    Vannini, Claudia; Galati, Stefano; Schweikert, Michael; Görtz, Hans-Dieter; Verni, Franco; Petroni, Giulio

    2013-01-01

    “Neglected Rickettsiaceae” (i.e. those harboured by non-hematophagous eukaryotic hosts) display greater phylogenetic variability and more widespread dispersal than pathogenic ones; yet, the knowledge about their actual host range and host shift mechanism is scarce. The present work reports the characterization following the full-cycle rRNA approach (SSU rRNA sequence, specific in situ hybridization, and ultrastructure) of a novel rickettsial bacterium, herewith proposed as 'Candidatus Megaira polyxenophila' gen. nov., sp. nov. We found it in association with four different free-living ciliates (Diophrys oligothrix, Euplotes octocarinatus, Paramecium caudatum, and Spirostomum sp., all belonging to Alveolata, Ciliophora); furthermore it was recently observed as intracellular occurring in Carteria cerasiformis and Pleodorina japonica (Chlorophyceae, Chlorophyta). Phylogenetic analyses demonstrated the belonging of the candidate new genus to the family Rickettsiaceae (Alphaproteobacteria, Rickettsiales) as a sister group of the genus Rickettsia. In situ observations revealed the ability of the candidate new species to colonize either nuclear or cytoplasmic compartments, depending on the host organism. The presence of the same bacterial species within different, evolutionary distant, hosts indicates that 'Candidatus Megaira polyxenophila' recently underwent several distinct host shifts, thus suggesting the existence of horizontal transmission pathways. We consider these findings as indicative of an unexpected spread of rickettsial infections in aquatic communities, possibly by means of trophic interactions, and hence propose a new interpretation of the origin and phylogenetic diversification of rickettsial bacteria. PMID:23977321

  15. Nubsella zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Sphingobacteriaceae isolated from freshwater.

    PubMed

    Asker, Dalal; Beppu, Teruhiko; Ueda, Kenji

    2008-03-01

    A yellow-pigmented, Gram-negative, strictly aerobic, rod-shaped bacterium (TDMA-5(T)) was isolated from a freshwater sample collected at Misasa (Tottori, Japan). The DNA G+C content was 38.6 mol%. Major fatty acids were iso-C(15 : 0), iso-C(17 : 0) 3-OH and summed feature 4 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c). MK-7 was the predominant respiratory quinone. Zeaxanthin was the major carotenoid pigment produced; flexirubin-type pigments were not produced. TDMA-5(T) was sensitive to gamma-irradiation. The strain degraded gelatin, casein, starch, Tween 80 and DNA. Phylogenetic analysis based on the 16S rRNA gene sequence placed TDMA-5(T) in a distinct lineage in the family Sphingobacteriaceae, sharing 89.4-93.4 % sequence similarity with members of the nearest genus Pedobacter. Strain TDMA-5(T) could be distinguished from the other members of the family Sphingobacteriaceae by a number of chemotaxonomic and phenotypic characteristics. Based on its unique phenotypic, genotypic and phylogenetic features, strain TDMA-5(T) represents a novel genus and species, for which the name Nubsella zeaxanthinifaciens gen. nov., sp. nov. is proposed. The type strain of Nubsella zeaxanthinifaciens is TDMA-5(T) (=NBRC 102579(T) =CCUG 54348(T)). PMID:18319463

  16. Haloalkaliphilic spore-forming sulfidogens from soda lake sediments and description of Desulfitispora alkaliphila gen. nov., sp. nov.

    PubMed Central

    Muyzer, Gerard

    2010-01-01

    An anaerobic enrichment with pyruvate as electron donor and thiosulfate at pH 10 and 0.6 M Na+ inoculated with pasteurized soda lake sediments resulted in a sulfidogenic coculture of two morphotypes of obligately anaerobic haloalkaliphilic endospore-forming clostridia, which were further isolated in pure culture. Strain AHT16 was a thin long rod able to ferment sugars and pyruvate and to respire H2, formate and pyruvate using thiosulfate and fumarate as electron acceptors and growing optimally at pH 9.5. Thiosulfate was reduced incompletely to sulfide and sulfite. The strain was closely related (99% sequence similarity) to a peptolytic alkaliphilic clostridium Natronincola peptidovorans. Strain AHT17 was a short rod with a restricted respiratory metabolism, growing with pyruvate and lactate as electron donor and sulfite, thiosulfate and elemental sulfur as electron acceptors with a pH optimum 9.5. Thiosulfate was reduced completely via sulfite to sulfide. The ability of AHT17 to use sulfite explained the stability of the original coculture of the two clostridia—one member forming sulfite from thiosulfate and another consuming it. Strain AHT17 formed an independent deep phylogenetic lineage within the Clostridiales and is proposed as a new genus and species Desulfitisporum alkaliphilum gen. nov., sp. nov. (=DSM 22410T = UNIQEM U794T). Electronic supplementary material The online version of this article (doi:10.1007/s00792-010-0310-y) contains supplementary material, which is available to authorized users. PMID:20364356

  17. Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine

    SciTech Connect

    Takai, Ken; Moser, Duane P.; Onstott, Tullis C.; Spoelstra, N; Pfiffner, Susan M.; Dohnalkova, Alice; Fredrickson, Jim K.

    2001-07-01

    A novel extreme alkaliphile was isolated from a mine water containment dam at 3.2 km bellow land surface in an ultra-deep gold mine near Carletonville, South Africa. The cells of this bacterium were straight to slightly curved rods, motile by flagella and formed endospores, Growth was observed over the temperature range 20-50 degreesC (optimum 40 degreesC; 45 min doubling time) and ph range 8.5-12.5 (optimum pH 10.0). The novel isolate, one of the most alkaliphilic micro-organisms yet described, was a strictly anaerobic chemo-organotroph capable of utilizing proteinaceous substrates such as yeast extract, peptone. tryptone and casein, Elemental sulfur, thiosulfate or fumarate, when included as accessory electron acceptors, improved growth. The G+C content of genomic DNA was 36.4 mol%, Phylogenetic analysis based on the 16S rDNA sequence indicated that the isolate is a member of cluster XI within the low G+C Cram-positive bacteria, but only distantly related to previously described members. On the basis of physiological and molecular properties, the isolate represents a novel species, for which the name Alkaliphilus transvaalensis gen. nov., sp. nov. is proposed (type strain SAGM1(T)= JCM 10712(T)= ATCC 700919(T)). The mechanism of generation of the highly alkaline microbial habitat and the possible source of the alkaliphile are discussed.

  18. Cipactlichthys scutatus, gen. nov., sp. nov. a New Halecomorph (Neopterygii, Holostei) from the Lower Cretaceous Tlayua Formation of Mexico

    PubMed Central

    Brito, Paulo M.; Alvarado-Ortega, Jesus

    2013-01-01

    Based on specimens from the Lower Cretaceous Tlayua Formation of Mexico, we describe a new genus and species of Halecomorphi, Cipactlichthysscutatus gen. et sp. nov, which exhibits several diagnostic characters such as the dermal bones and the scales with ganoin and highly ornamented by numerous tubercles and ridges; parietal slightly longer than wide with approximately the same length as the frontal; jaws extending far, below the posterior orbital margin, reaching the posterior third of the postorbital plate; maxilla with a convexly rounded posterior margin; pectoral fin margins slightly convex; first ray of pectoral fin very long, reaching the posterior edge of the pelvic fin; about 37 preural vertebrae and 7 Ural centra; a series of hypertrophied scales just posterior to the cleithrum; arrangement of flank scales with two rows of deep scales; a series of dorsal and ventral scutes forming the dorsal and ventral midline, between the dorsal and anal fins and the caudal fin. A phylogenetic analysis including two outgroups and eleven neopterygians confirmed the monophyly of the Holostei as well as the monophyly of the Halecomorphi, although this last clade is weakly supported. Cipactlichthysscutatus was hypothesised as the sister-group of the (Ionoscopiformes + Amiiformes). PMID:24023885

  19. Desulfohalophilus alkaliarsenatis gen. nov., sp. nov., an extremely halophilic sulfate- and arsenate-respiring bacterium from Searles Lake, California

    USGS Publications Warehouse

    Blum, Jodi Switzer; Kulp, Thomas R.; Han, Sukkyun; Lanoil, Brian; Saltikov, Chad W.; Stolz, John F.; Miller, Laurence G.; Oremland, Ronald S.

    2012-01-01

    A haloalkaliphilic sulfate-respiring bacterium, strain SLSR-1, was isolated from a lactate-fed stable enrichment culture originally obtained from the extreme environment of Searles Lake, California. The isolate proved capable of growth via sulfate-reduction over a broad range of salinities (125–330 g/L), although growth was slowest at salt-saturation. Strain SLSR-1 was also capable of growth via dissimilatory arsenate-reduction and displayed an even broader range of salinity tolerance (50–330 g/L) when grown under these conditions. Strain SLSR-1 could also grow via dissimilatory nitrate reduction to ammonia. Growth experiments in the presence of high borate concentrations indicated a greater sensitivity of sulfate-reduction than arsenate-respiration to this naturally abundant anion in Searles Lake. Strain SLSR-1 contained genes involved in both sulfate-reduction (dsrAB) and arsenate respiration (arrA). Amplicons of 16S rRNA gene sequences obtained from DNA extracted from Searles Lake sediment revealed the presence of close relatives of strain SLSR-1 as part of the flora of this ecosystem despite the fact that sulfate-reduction activity could not be detected in situ. We conclude that strain SLSR-1 can only achieve growth via arsenate-reduction under the current chemical conditions prevalent at Searles Lake. Strain SLSR-1 is a deltaproteobacterium in the family Desulfohalobiacea of anaerobic, haloalkaliphilic bacteria, for which we propose the name Desulfohalophilus alkaliarsenatis gen. nov., sp. nov.

  20. Rubritalea marina gen. nov., sp. nov., a marine representative of the phylum 'Verrucomicrobia', isolated from a sponge (Porifera).

    PubMed

    Scheuermayer, Matthias; Gulder, Tobias A M; Bringmann, Gerhard; Hentschel, Ute

    2006-09-01

    A marine bacterium, strain Pol012(T), was isolated from the Mediterranean sponge Axinella polypoides and subsequently characterized as belonging to subphylum 1 of the phylum 'Verrucomicrobia'. Strain Pol012(T) was non-motile, Gram-negative, coccoid or rod-shaped and red in colour. The menaquinones MK-8 and MK-9 were detected. The G+C content of the genomic DNA was 50.9 mol%. Growth was possible at temperatures between 8 and 30 degrees C and at pH values between 6.8 and 8.2. The closest cultured relative of strain Pol012(T) was Akkermansia muciniphila (83 % sequence similarity), while the closest environmental 16S rRNA gene sequence was the marine clone Arctic96BD-2 (95 % sequence similarity). Strain Pol012(T) is the first marine pure-culture representative of 'Verrucomicrobia' subphylum 1 and represents a novel genus and species, for which the name Rubritalea marina gen. nov., sp. nov. is proposed. The type strain is Pol012(T) (=DSM 177716(T)=CIP 108984(T)). PMID:16957108

  1. Rouxiella chamberiensis gen. nov., sp. nov., a member of the family Enterobacteriaceae isolated from parenteral nutrition bags.

    PubMed

    Le Flèche-Matéos, Anne; Levast, Marion; Lomprez, Fabienne; Arnoux, Yolande; Andonian, Clément; Perraud, Michel; Vincent, Véronique; Ar Gouilh, Meriadeg; Thiberge, Jean-Michel; Vandenbogaert, Mathias; Diancourt, Laure; Caro, Valérie; Burguière, Ana Maria; Manuguerra, Jean-Claude

    2015-06-01

    Parenteral nutrition bags for newborns were found contaminated by a previously undescribed member of the family Enterobacteriaceae. The six isolates studied by rrs gene (encoding 16S rRNA) sequence analysis and multi-locus sequence analysis (MLSA) formed a discrete branch close to the genera Ewingella, Rahnella, Yersinia,Hafnia and Serratia. Phenotypically, the new taxon was distinct from these five genera. The new taxon gave positive results in Voges-Proskauer, Simmons citrate and o-nitrophenyl-?-galactoside hydrolysis tests; fermented d-glucose, d-mannitol, l-rhamnose, melibiose, l-arabinose and d-xylose; hydrolysed aesculin; and did not ferment maltose, trehalose, raffinose, d-sorbitol, sucrose or cellobiose. Tests for motility, gas production, urease, gelatinase and nitrate reduction were also negative. All isolates failed to grow at 37 °C. The DNA G+C content of strain 130333T was 53 mol%. On the basis of data obtained in this study, the six isolates represent a novel species of a new genus in the family Enterobacteriaceae, named Rouxiella chamberiensis gen. nov., sp. nov. The type strain of the type species is 130333T (?= CIP 110714T = DSM 28324T). PMID:25747423

  2. Phylogenetic analysis identifies the 'megabacterium' of birds as a novel anamorphic ascomycetous yeast, Macrorhabdus ornithogaster gen. nov., sp. nov.

    PubMed

    Tomaszewski, Elizabeth K; Logan, Kathleen S; Snowden, Karen F; Kurtzman, Cletus P; Phalen, David N

    2003-07-01

    An organism commonly referred to as 'megabacterium' colonizes the gastric isthmus of many species of birds. It is weakly gram-positive and periodic acid-Schiff-positive and stains with silver stains. Previous studies have shown that it has a nucleus and a cell wall similar to those seen in fungi. Calcofluor white M2R staining suggests that the cell wall contains chitin, a eukaryote-specific substance, and rRNA in situ hybridization demonstrates that it is a eukaryote. To characterize this organism phylogenetically, DNA was extracted from purified cells. rDNA was readily amplified by PCR with pan-fungal DNA primer sets and primer sets derived from the newly determined sequence, but not with bacteria-specific primer sets. Specific primer sets amplified rDNA from isthmus scrapings from an infected bird, but not from a non-infected bird or other control DNA. The sequence was confirmed to derive from the purified organism by in situ rRNA hybridization using a specific probe. Phylogenetic analysis of sequences of the 18S rDNA and domain D1/D2 of 26S rDNA showed the organism to be a previously undescribed anamorphic ascomycetous yeast representing a new genus. The name Macrorhabdus ornithogaster gen. nov., sp. nov. is proposed for this organism. The type material is CBS 9251T (= NRRL Y-27487T). PMID:12892150

  3. Iapetonudus (N. gen.) and Iapetognathus Landing, unusual Earliest Ordovician multielement conodont taxa and their utility for biostratigraphy

    USGS Publications Warehouse

    Nicoll, R.S.; Miller, J.F.; Nowlan, G.S.; Repetski, J.E.; Ethington, Raymond L.

    1999-01-01

    The Early Ordovician (Tremadocian) multielement conodont genus Iapetognathus is one of the oldest denticulate euconodont genera known. The ramiform-ramiform apparatus structure of Iapetognathus is not similar morphologically to other Late Cambrian to Earliest Ordovician denticulate multielement taxa, such as Eodentatus or Cordyloduts, because the major denticulate process has a lateral rather than a posterior orientation as it is in the other two examples. For this reason the genus is believed to have developed from the coniform-coniform apparatus Iapetonudus ibexensis (N.gen., n.sp.) through the development of the denticulate lateral processes. The two genera have a number of morphologic features in common and appear in stratigraphic succession. Iapetognathus aengensis (Lindstro??m) is redefined as a multielement taxon using topotype material and Ig. preaengensis Landing is placed in synonymy with it. Iapetognathus sprakersi, recently described by Landing in Landing and others (1996), is recognized as a multielement species and the new multielement species, Ig. fluctivagus, Ig. jilinensis and Ig. landingi n. spp. are described herein, based on type specimens from Utah (U.S.A.), Jilin (China) and Colorado (U.S.A.) respectively. Iapetonudus and Iapetognathus are important genera in defining the level of the Cambrian-Ordovician boundary. Iapetonudus is currently recognized only from Utah, Texas and Oklahoma, but Iapetognathus is cosmopolitan in its distribution.

  4. Feifantangia zhejiangensis gen. nov., sp. nov., a marine bacterium isolated from seawater of the East China Sea.

    PubMed

    Zheng, Gang; Chen, Zuo-Guo; Jiang, Ri-Jin; Yang, Zhi-Jian

    2015-12-01

    A marine bacterium, NMD7(T), was isolated from seawater of the East China Sea. The cells were found to be aerobic, Gram-stain negative, non-motile rods. Growth of strain NMD7(T) could be observed in the medium without Na(+). Flexirubin-type pigments were observed to be produced. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NMD7(T) is an authentic member of the Cytophaga-Flavobacterium-Bacteroides phylum, forming a monophyletic clade as retrieved in neighbor-joining, maximum-likelihood and maximum-parsimony phylogenetic trees, and is closely related to Formosa spongicola A2(T) (96.0 %). The predominant respiratory quinone was determined to be MK-6. Major cellular fatty acids were identified as iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH. The main polar lipids were found to consist of phosphatidylethanolamine, one aminophospholipid, three aminolipids and five unidentified lipids. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, it is proposed that strain NMD7(T) be classified as representing a new genus, Feifantangia gen. nov. and a new species, Feifantangia zhejiangensis sp. nov. The type strain is NMD7(T) (=KCTC 42445T =MCCC 1K00458T). PMID:26410371

  5. Imperialibacter roseus gen. nov., sp. nov., a novel bacterium of the family Flammeovirgaceae isolated from Permian groundwater.

    PubMed

    Wang, Hui; Li, Junde; Zheng, Tianling; Hill, Russell T; Hu, Xiaoke

    2013-11-01

    A novel bacterial strain, designated P4(T), was isolated from Permian groundwater and identified on the basis of its phylogenetic, genotypic, chemotaxonomic and phenotypic characteristics. Cells were aerobic, Gram-stain-negative rods. 16S rRNA gene sequence-based phylogenetic analysis revealed that P4(T) is affiliated with the family Flammeovirgaceae in the phylum Bacteroidetes, but forms a distinct cluster within this family. The DNA G+C content of strain P4(T) was 45.2 mol%. The predominant cellular fatty acids were C16?:?1?6c/C16?:?1?7c and iso-C15?:?0. MK-7 was the main respiratory quinone. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, unidentified phospholipids, an unidentified aminolipid, unidentified glycolipids and unidentified polar lipids. Based on our extensive polyphasic analysis, a novel species in a new genus, Imperialibacter roseus gen. nov., sp. nov., is proposed. The type strain of Imperialibacter roseus is P4(T) (?=?CICC 10659(T)?=?KCTC 32399(T)). PMID:23749281

  6. Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine.

    PubMed

    Takai, K; Moser, D P; Onstott, T C; Spoelstra, N; Pfiffner, S M; Dohnalkova, A; Fredrickson, J K

    2001-07-01

    A novel extreme alkaliphile was isolated from a mine water containment dam at 3.2 km below land surface in an ultra-deep gold mine near Carletonville, South Africa. The cells of this bacterium were straight to slightly curved rods, motile by flagella and formed endospores. Growth was observed over the temperature range 20-50 degrees C (optimum 40 degrees C; 45 min doubling time) and pH range 8.5-12.5 (optimum pH 10.0). The novel isolate, one of the most alkaliphilic micro-organisms yet described, was a strictly anaerobic chemo-organotroph capable of utilizing proteinaceous substrates such as yeast extract, peptone, tryptone and casein. Elemental sulfur, thiosulfate or fumarate, when included as accessory electron acceptors, improved growth. The G+C content of genomic DNA was 36.4 mol %. Phylogenetic analysis based on the 16S rDNA sequence indicated that the isolate is a member of cluster XI within the low G+C gram-positive bacteria, but only distantly related to previously described members. On the basis of physiological and molecular properties, the isolate represents a novel species, for which the name Alkaliphilus transvaalensis gen. nov., sp. nov. is proposed (type strain SAGM1T = JCM 10712T = ATCC 700919T). The mechanism of generation of the highly alkaline microbial habitat and the possible source of the alkaliphile are discussed. PMID:11491320

  7. Gelidivirgula Patagoniensis Gen. Nov., Sp. Nov., A Novel Psychrotolerant, Sporeforming Anaerobe Isolated from Magellanic Penguin Guano in Patagonia, Chile

    NASA Technical Reports Server (NTRS)

    Pikuta, Elena V.; Hoover, Richard B.; Marsic, Damien; Whitman, William B.; Tang, Jane; Krader, Paul

    2003-01-01

    A novel obligately anaerobic, psychrotrophic bacterium, strain PPP2(sup T), was isolated from guano of the Magellanic penguin (Spheniscus magellanicus) in Patagonia, Chile. The Gram-positive, sporeforming, straight rods with sizes 0.6-0.9 x 3.0-5.0 microns, are motile by peritrichous flagella. Growth was observed to occur within the pH range 6.0-9.5 (optimum pH x), and temperature range 2-28 C (optimum 20 C). The novel isolate does not require NaCl for growth, but is halotolerant and growth was observed between 0 and 7 % NaCl (w/v) with optimum at 0.5 % (w/v). The new isolate is a catalase negative chemoorganohetherotroph with fermentative metabolism and uses as substrates: peptone, Bacto-tryptone, Casamino acids, and yeast extract. The major metabolic products are: acetate, butyrate, ethanol, and hydrogen is a minor gas product.. Strain PPP2 was sensitive to ampicillin, tetracycline, chloramphenicol, rifampin, kanamycin, and gentamycin. The G+C content of the DNA is 43.6 mol%. On the basis of 16S rDNA gene sequences and phenotypic characteristics, it is proposed that the strain PPP2(sup T) (= ATCC BAA-755(sup T) = JSM ...(sup T)) is assigned to the new genus Gelidivirgula gen. nov., as a representative of the new species, Gelidivirgula patagonensis sp. nov.

  8. Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum 'Verrucomicrobia' isolated from seawater in Japan.

    PubMed

    Yoon, Jaewoo; Yasumoto-Hirose, Mina; Katsuta, Atsuko; Sekiguchi, Hiroshi; Matsuda, Satoru; Kasai, Hiroaki; Yokota, Akira

    2007-05-01

    An obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium, designated strain 04OKA010-24(T), was isolated from seawater surrounding the hard coral Galaxea fascicularis L., collected at Majanohama, Akajima, Japan, and was subjected to a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that the new strain represented a member of the phylum 'Verrucomicrobia' and shared 84-95 % sequence similarity with cultivated strains of 'Verrucomicrobia' subdivision 4. Amino acid analysis of the cell-wall hydrolysate indicated the absence of muramic acid and diaminopimelic acid, which suggested that the strain did not contain peptidoglycan in the cell wall. The G+C content of the DNA was 53.9 mol%. MK-7 was the major menaquinone and C(14 : 0), C(18 : 1)omega9c and C(18 : 0) were the major fatty acids. On the basis of these data, it was concluded that strain 04OKA010-24(T) represents a novel species in a new genus in subdivision 4 of the phylum 'Verrucomicrobia', for which the name Coraliomargarita akajimensis gen. nov., sp. nov. is proposed. The type strain of Coraliomargarita akajimensis is 04OKA010-24(T) (=MBIC06463(T)=IAM 15411(T)=KCTC 12865(T)). PMID:17473241

  9. Factors Influencing the Decisions and Actions of Pilots and Air Traffic Controllers in Three Plausible NextGen Environments

    NASA Technical Reports Server (NTRS)

    Vu, Kim-Phuong L.; Strybel, Thomas Z.; Battiste, Vernol; Johnson, Walter

    2011-01-01

    In the current air traffic management (ATM) system, pilots and air traffic controllers have well-established roles and responsibilities: pilots fly aircraft and are concerned with energy management, fuel efficiency, and passenger comfort; controllers separate aircraft and are concerned with safety and management of traffic flows. Despite having different goals and obligations, both groups must be able to effectively communicate and interact with each other for the ATM system to work. This interaction will become even more challenging as traffic volume increases dramatically in the near future. To accommodate this increase, by 2025 the national air transportation system in the U.S. will go through a transformation that will modernize the ATM system and make it safer, more effective, and more efficient. This new system, NextGen, will change how pilots and controllers perform their tasks by incorporating advanced technologies and employing new procedures. It will also distribute responsibility between pilots, controllers and automation over such tasks as maintaining aircraft separation. The present chapter describes three plausible concepts of operations that allocate different ATM responsibilities to these groups. We describe how each concept changes the role of each operator and the types of decisions and actions performed by them.

  10. Thermogutta terrifontis gen. nov., sp. nov. and Thermogutta hypogea sp. nov., thermophilic anaerobic representatives of the phylum Planctomycetes.

    PubMed

    Slobodkina, Galina B; Kovaleva, Olga L; Miroshnichenko, Margarita L; Slobodkin, Alexander I; Kolganova, Tatyana V; Novikov, Andrei A; van Heerden, Esta; Bonch-Osmolovskaya, Elizaveta A

    2015-03-01

    Two novel strains of thermophilic planctomycetes were recovered from terrestrial and subterranean habitats. Strain R1(T) was isolated from a hot spring (Kunashir Island, Russia) and strain SBP2(T) was isolated from a deep gold mine (South Africa). Both isolates grew in the temperature range 30-60 °C and pH range 5.0-8.0. Strain R1(T) grew optimally at 60 °C and pH 6.0-6.5; for SBP2(T) optimal conditions were at 52 °C and pH 7.5-8.0. Both strains were capable of anaerobic respiration with nitrate and nitrite as electron acceptors as well as of microaerobic growth. They also could grow by fermentation of mono-, di- and polysaccharides. Based on their phylogenetic position and phenotypic features we suggest that the new isolates represent two novel species belonging to a new genus in the order Planctomycetales, for which the names Thermogutta terrifontis gen. nov., sp. nov. and Thermogutta hypogea sp. nov. are proposed. The type strain of Thermogutta terrifontis, the type species of the genus, is R1(T) (?=?DSM 26237(T)?=?VKM B-2805(T)), and the type strain of Thermogutta hypogea is SBP2(T) (?=?JCM 19991(T)?=?VKM B-2782(T)). PMID:25479950

  11. Aminiphilus circumscriptus gen. nov., sp. nov., an anaerobic amino-acid-degrading bacterium from an upflow anaerobic sludge reactor.

    PubMed

    Díaz, C; Baena, S; Fardeau, M-L; Patel, B K C

    2007-08-01

    Strain ILE-2(T) was isolated from an upflow anaerobic sludge bed reactor treating brewery wastewater. The motile, non-sporulating, slightly curved cells (2-4 x 0.1 microm) stained Gram-negative and grew optimally at 42 degrees C and pH 7.1 with 0.5 % NaCl. The strain required yeast extract for growth and fermented Casamino acids, peptone, isoleucine, arginine, lysine, alanine, valine, glutamate, histidine, glutamine, methionine, malate, fumarate, glycerol and pyruvate to acetate, propionate and minor amounts of branched-chain fatty acids. Carbohydrates, formate, acetate, propionate, butyrate, isovalerate, methanol, ethanol, 1-propanol, butanol, lactate, succinate, starch, casein, gelatin, xylan and a number of other amino acids were not utilized. The DNA G+C content of strain ILE-2(T) was 52.7 mol%. 16S rRNA gene sequence analysis revealed that ILE-2(T) was distantly related to members of the genera Aminobacterium (83 % similarity) and Aminomonas (85 % similarity) in the family Syntrophomonadaceae, order Clostridiales, phylum Firmicutes. On the basis of the results of our polyphasic analysis, strain ILE-2(T) represents a novel species and genus within the family Syntrophomonadaceae, for which the name Aminiphilus circumscriptus gen. nov., sp. nov. is proposed. The type strain of Aminiphilus circumscriptus is ILE-2(T) (=DSM 16581(T) =JCM 14039(T)). PMID:17684281

  12. The eGenVar data management system—cataloguing and sharing sensitive data and metadata for the life sciences

    PubMed Central

    Razick, Sabry; Mo?nik, Rok; Thomas, Laurent F.; Ryeng, Einar; Drabløs, Finn; Sætrom, Pål

    2014-01-01

    Systematic data management and controlled data sharing aim at increasing reproducibility, reducing redundancy in work, and providing a way to efficiently locate complementing or contradicting information. One method of achieving this is collecting data in a central repository or in a location that is part of a federated system and providing interfaces to the data. However, certain data, such as data from biobanks or clinical studies, may, for legal and privacy reasons, often not be stored in public repositories. Instead, we describe a metadata cataloguing system and a software suite for reporting the presence of data from the life sciences domain. The system stores three types of metadata: file information, file provenance and data lineage, and content descriptions. Our software suite includes both graphical and command line interfaces that allow users to report and tag files with these different metadata types. Importantly, the files remain in their original locations with their existing access-control mechanisms in place, while our system provides descriptions of their contents and relationships. Our system and software suite thereby provide a common framework for cataloguing and sharing both public and private data. Database URL: http://bigr.medisin.ntnu.no/data/eGenVar/ PMID:24682735

  13. The effects of angiotensinogen gene polymorphisms on cardiovascular disease outcomes during antihypertensive treatment in the GenHAT study

    PubMed Central

    Do, Anh N.; Irvin, Marguerite R.; Lynch, Amy I.; Claas, Steven A.; Boerwinkle, Eric; Davis, Barry R.; Ford, Charles E.; Eckfeldt, John H.; Tiwari, Hemant K.; Limdi, Nita A.; Arnett, Donna K.

    2014-01-01

    Previous studies have reported that risk of cardiovascular morbidity and mortality substantially increases in hypertensive patients, especially among those with inadequate blood pressure control. Two common antihypertensive drug classes including thiazide diuretics and angiotensin-converting enzyme (ACE) inhibitors affect different enzymes in the renin-angiotensin-aldosterone system (RAAS). In the RAAS, angiotensinogen is converted into angiotensin II which increases blood pressure through vasoconstriction. Using a case-only design with 3448 high-risk hypertensive individuals from the Genetics of Hypertension Associated Treatment (GenHAT) study, we examined whether seven single nucleotide polymorphisms (SNPs) in the angiotensinogen gene (AGT) interact with three classes of antihypertensive drugs including chlorthalidone (a thiazide diuretic), lisinopril (an ACE inhibitor), and amlodipine (a calcium channel blocker) to modify the risk of incident coronary heart disease (CHD) and heart failure (HF) among Caucasian and African American participants, separately. We found no gene by treatment interactions to be statistically significant after correction for multiple testing. However, some suggestive results were found. African American participants with the minor allele of rs11122576 had over two-fold higher risk of CHD when using chlorthalidone compared to using amlodipine, or lisinopril compared to amlodipine (p = 0.006 and p = 0.01, respectively). Other marginal associations are also reported among both race groups. The findings reported here suggest that rs11122576 could contribute to future personalization of antihypertensive treatment among African Americans though more studies are needed. PMID:25278896

  14. Gen-Struktur und Gen-Expression

    NASA Astrophysics Data System (ADS)

    Schütz, Günther

    1981-04-01

    In the chicken oviduct the synthesis of the egg-white proteins ovalbumin, conalbumin, ovomucoid and lysozyme is controlled by the female sex steroids. The steroid-controlled rate of synthesis of these proteins is closely correlated to the cellular concentration of the egg-white protein mRNAs. The accumulation of these mRNAs is achieved by a drecreased rate of degradation and an increased rate of synthesis. To understand the molecular mechanism that regulates the expression of this group of genes we have isolated the lysozyme and ovomucoid gene by gene-cloning. The structure and expression of the lysozyme gene has been studied.

  15. Cobbania corrugata gen. et comb. nov. (Araceae): a floating aquatic monocot from the Upper Cretaceous of western North America.

    PubMed

    Stockey, Ruth A; Rothwell, Gar W; Johnson, Kirk R

    2007-04-01

    The fossil record of aquatic flowering plants broadens our understanding of their former diversity and origins from terrestrial ancestors. This paper describes a floating aquatic monocot from 71 whole plants and several isolated leaf fragments from Upper Cretaceous oxbow lake sediments in the Dinosaur Park Formation, Alberta, Canada. The new material is represented by rosettes of leaves and roots attached to short stems that are interconnected by stolons and corresponds to the fossil aroid originally described as Pistia corrugata Lesquereux. Up to six plants have been found interconnected on a single slab suggesting that these plants grew in extensive floating mats covering lakes and calm stretches of rivers. Stems have up to six leaves and large numbers of branched aquatic roots. The leaf is trumpet-shaped with an elongate clasping petiole, large aerenchymatous base, and a nearly circular blade rim. Leaf bases are often filled with sediment giving the leaf the appearance of having a basal pouch. Petioles have 6-9 veins that divide into an upper and lower set, and veins converge at an apical notch. A submarginal collective vein and at least two marginal veins with branching veins form the leaf rim. A series of dichotomizing and anastomosing veins characterize the adaxial leaf surface. Tertiary and quaternary veins form polygonal areolae. Leaf surfaces are covered in trichomes that, like those in Pistia stratiotes, probably aided in buoyancy. A reconstruction of the plant is presented. Based on unique leaf morphology, these fossil plants are clearly not assignable to the genus Pistia and are described as Cobbania corrugata (Lesquereux) Stockey, Rothwell et Johnson gen. et comb. nov. Recent systematic analyses using molecular characters resolve two separate origins of floating aquatic aroids included in the duckweeds and the genus Pistia. This new fossil genus increases our understanding of colonization of aquatic habitats by revealing a third possible origin of the floating aquatic habit within Araceae. PMID:21636430

  16. A New Troodontid Theropod, Talos sampsoni gen. et sp. nov., from the Upper Cretaceous Western Interior Basin of North America

    PubMed Central

    Zanno, Lindsay E.; Varricchio, David J.; O'Connor, Patrick M.; Titus, Alan L.; Knell, Michael J.

    2011-01-01

    Background Troodontids are a predominantly small-bodied group of feathered theropod dinosaurs notable for their close evolutionary relationship with Avialae. Despite a diverse Asian representation with remarkable growth in recent years, the North American record of the clade remains poor, with only one controversial species—Troodon formosus—presently known from substantial skeletal remains. Methodology/Principal Findings Here we report a gracile new troodontid theropod—Talos sampsoni gen. et sp. nov.—from the Upper Cretaceous Kaiparowits Formation, Utah, USA, representing one of the most complete troodontid skeletons described from North America to date. Histological assessment of the holotype specimen indicates that the adult body size of Talos was notably smaller than that of the contemporary genus Troodon. Phylogenetic analysis recovers Talos as a member of a derived, latest Cretaceous subclade, minimally containing Troodon, Saurornithoides, and Zanabazar. MicroCT scans reveal extreme pathological remodeling on pedal phalanx II-1 of the holotype specimen likely resulting from physical trauma and subsequent infectious processes. Conclusion/Significance Talos sampsoni adds to the singularity of the Kaiparowits Formation dinosaur fauna, which is represented by at least 10 previously unrecognized species including the recently named ceratopsids Utahceratops and Kosmoceratops, the hadrosaurine Gryposaurus monumentensis, the tyrannosaurid Teratophoneus, and the oviraptorosaurian Hagryphus. The presence of a distinct troodontid taxon in the Kaiparowits Formation supports the hypothesis that late Campanian dinosaurs of the Western Interior Basin exhibited restricted geographic ranges and suggests that the taxonomic diversity of Late Cretaceous troodontids from North America is currently underestimated. An apparent traumatic injury to the foot of Talos with evidence of subsequent healing sheds new light on the paleobiology of deinonychosaurians by bolstering functional interpretations of prey grappling and/or intraspecific combat for the second pedal digit, and supporting trackway evidence indicating a minimal role in weight bearing. PMID:21949721

  17. Cetia pacifica gen. nov., sp. nov., a chemolithoautotrophic, thermophilic, nitrate-ammonifying bacterium from a deep-sea hydrothermal vent.

    PubMed

    Grosche, Ashley; Sekaran, Hema; Pérez-Rodríguez, Ileana; Starovoytov, Valentin; Vetriani, Costantino

    2015-04-01

    A thermophilic, anaerobic, chemolithoautotrophic bacterium, strain TB-6(T), was isolated from a deep-sea hydrothermal vent located on the East Pacific Rise at 9° N. The cells were Gram-staining-negative and rod-shaped with one or more polar flagella. Cell size was approximately 1-1.5 µm in length and 0.5 µm in width. Strain TB-6(T) grew between 45 and 70 °C (optimum 55-60 °C), 0 and 35 g NaCl l(-1) (optimum 20-30 g l(-1)) and pH 4.5 and 7.5 (optimum pH 5.5-6.0). Generation time under optimal conditions was 2 h. Growth of strain TB-6(T) occurred with H2 as the energy source, CO2 as the carbon source and nitrate or sulfur as electron acceptors, with formation of ammonium or hydrogen sulfide, respectively. Acetate, (+)-d-glucose, Casamino acids, sucrose and yeast extract were not used as carbon and energy sources. Inhibition of growth occurred in the presence of lactate, peptone and tryptone under a H2/CO2 (80?:?20; 200 kPa) gas phase. Thiosulfate, sulfite, arsenate, selenate and oxygen were not used as electron acceptors. The G+C content of the genomic DNA was 36.8 mol%. Phylogenetic analysis of the 16S rRNA gene of strain TB-6(T) showed that this organism branched separately from the three most closely related genera, Caminibacter , Nautilia and Lebetimonas , within the family Nautiliaceae . Strain TB-6(T) contained several unique fatty acids in comparison with other members of the family Nautiliaceae . Based on experimental evidence, it is proposed that the organism represents a novel species and genus within the family Nautiliaceae , Cetia pacifica, gen. nov., sp. nov. The type strain is TB-6(T) (?=?DSM 27783(T)?=?JCM 19563(T)). PMID:25604337

  18. Thermoterrabacterium ferrireducens gen. nov., sp. nov., a thermophilic anaerobic dissimilatory Fe(III)-reducing bacterium from a continental hot spring.

    PubMed

    Slobodkin, A; Reysenbach, A L; Strutz, N; Dreier, M; Wiegel, J

    1997-04-01

    A strain of a thermophilic, anaerobic, dissimilatory, Fe(III)-reducing bacterium, Thermoterrabacterium ferrireducens gen. nov., sp. nov. (type strain JW/AS-Y7T; DSM 11255), was isolated from hot springs in Yellowstone National Park and New Zealand. The gram-positive-staining cells occurred singly or in pairs as straight to slightly curved rods, 0.3 to 0.4 by 1.6 to 2.7 microns, with rounded ends and exhibited a tumbling motility. Spores were not observed. The temperature range for growth was 50 to 74 degrees C with an optimum at 65 degrees C. The pH range for growth at 65 degrees C was from 5.5 to 7.6, with an optimum at 6.0 to 6.2. The organism coupled the oxidation of glycerol to reduction of amorphous Fe(III) oxide or Fe(III) citrate as an electron acceptor. In the presence as well as in the absence of Fe(III) and in the presence of CO2, glycerol was metabolized by incomplete oxidation to acetate as the only organic metabolic product; no H2 was produced during growth. The organism utilized glycerol, lactate, 1,2-propanediol, glycerate, pyruvate, glucose, fructose, mannose, and yeast extract as substrates. In the presence of Fe(III) the bacterium utilized molecular hydrogen. The organism reduced 9,10-anthraquinone-2,6-disulfonic acid, fumarate (to succinate), and thiosulfate (to elemental sulfur) but did not reduce MnO2, nitrate, sulfate, sulfite, or elemental sulfur. The G + C content of the DNA was 41 mol% (as determined by high-performance liquid chromatography). The 16S ribosomal DNA sequence analysis placed the isolated strain as a member of a new genus within the gram-type-positive Bacillus-Clostridium subphylum. PMID:9103646

  19. Proof-of-Concept of a Networked Validation Environment for Distributed Air/Ground NextGen Concepts

    NASA Technical Reports Server (NTRS)

    Grisham, James; Larson, Natalie; Nelson, Justin; Reed, Joshua; Suggs, Marvin; Underwood, Matthew; Papelis, Yiannis; Ballin, Mark G.

    2013-01-01

    The National Airspace System (NAS) must be improved to increase capacity, reduce flight delays, and minimize environmental impacts of air travel. NASA has been tasked with aiding the Federal Aviation Administration (FAA) in NAS modernization. Automatic Dependent Surveillance-Broadcast (ADS-B) is an enabling technology that is fundamental to realization of the Next Generation Air Transportation System (NextGen). Despite the 2020 FAA mandate requiring ADS-B Out equipage, airspace users are lacking incentives to equip with the requisite ADS-B avionics. A need exists to validate in flight tests advanced concepts of operation (ConOps) that rely on ADS-B and other data links without requiring costly equipage. A potential solution is presented in this paper. It is possible to emulate future data link capabilities using the existing in-flight Internet and reduced-cost test equipment. To establish proof-of-concept, a high-fidelity traffic operations simulation was modified to include a module that simulated Internet transmission of ADS-B messages. An advanced NASA ConOp, Flight Deck Interval Management (FIM), was used to evaluate technical feasibility. A preliminary assessment of the effects of latency and dropout rate on FIM was performed. Flight hardware that would be used by proposed test environment was connected to the simulation so that data transfer from aircraft systems to test equipment could be verified. The results indicate that the FIM ConOp, and therefore, many other advanced ConOps with equal or lesser response characteristics and data requirements, can be evaluated in flight using the proposed concept.

  20. Hoplitolyda duolunica gen. et sp. nov. (Insecta, Hymenoptera, Praesiricidae), the Hitherto Largest Sawfly from the Mesozoic of China

    PubMed Central

    Gao, Taiping; Shih, Chungkun; Rasnitsyn, Alexandr P.; Ren, Dong

    2013-01-01

    Background Large body size of an insect, in general, enhances its capability of predation, competition, and defense, resulting in better survivability and reproduction. Hymenopterans, most being phytophagous or parasitic, have a relatively small to medium body size, typically under 50.0 mm in body length. Principal Findings Herein, we describe Hoplitolyda duolunica gen. et sp. nov., assigned to Praesiricidae, from the Early Cretaceous Yixian Formation of China. This new species is the largest fossil hymenopteran hitherto with body estimated >55.0 mm long and wing span >92.0 mm. H. duolunica is, to our knowledge, the only sawfly with Sc present in the hind wing but not in the forewing. Its Rs1 and M1 meeting each other at 145° angle represents an intermediate in the transition from “Y” to “T” shapes. Even though Hoplitolyda differs significantly from all previously described genera in two subfamilies of Praesricidae, we leave the new genus unplaced in existing subfamilies, pending discovery of material with more taxonomic structure. Conclusions/Significance Hoplitolyda has many unique and interesting characters which might have benefitted its competition, survival, and reproduction: large body size and head with robust and strong mandibles for defense and/or sexual selection, unique wing venation and setal arrangements for flight capability and mobility, dense hairs on body and legs for sensing and protection, etc. Considering the reported ferocious predators of feathered dinosaurs, pterosaurs, birds, and mammals coexisting in the same eco-system, Hoplitolyda is an interesting case of “survival of the fittest” in facing its evolutionary challenges. PMID:23671596

  1. Limisphaera ngatamarikiensis gen. nov., sp. nov., a thermophilic, pink-pigmented coccus isolated from subaqueous mud of a geothermal hotspring.

    PubMed

    Anders, Heike; Power, Jean F; MacKenzie, Andrew D; Lagutin, Kirill; Vyssotski, Mikhail; Hanssen, Eric; Moreau, John W; Stott, Matthew B

    2015-04-01

    A novel bacterial strain, NGM72.4(T), was isolated from a hot spring in the Ngatamariki geothermal field, New Zealand. Phylogenetic analysis based on 16S rRNA gene sequences grouped it into the phylum Verrucomicrobia and class level group 3 (also known as OPB35 soil group). NGM72.4(T) stained Gram-negative, and was catalase- and oxidase-positive. Cells were small cocci, 0.5-0.8 µm in diameter, which were motile by means of single flagella. Transmission electron micrograph (TEM) imaging showed an unusual pirellulosome-like intracytoplasmic membrane. The peptidoglycan content was very small with only trace levels of diaminopimelic acid detected. No peptidoglycan structure was visible in TEM imaging. The predominant isoprenoid quinone was MK-7 (92%). The major fatty acids (>15%) were C(16?:?0), anteiso-C(15?:?0), iso-C(16?:?0) and anteiso-C(17?:?0). Major phospholipids were phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME) and cardiolipin (CL), and a novel analogous series of phospholipids where diacylglycerol was replaced with diacylserinol (sPE, sPMME, sCL). The DNA G+C content was 65.6 mol%. Cells displayed an oxidative chemoheterotrophic metabolism. NGM72.4(T) is a strictly aerobic thermophile (growth optimum 60-65 °C), has a slightly alkaliphilic pH growth optimum (optimum pH 8.1-8.4) and has a NaCl tolerance of up to 8 g l(-1). Colonies were small, circular and pigmented pale pink. The distinct phylogenetic position and phenotypic traits of strain NGM72.4(T) distinguish it from all other described species of the phylum Verrucomicrobia and, therefore, it is considered to represent a novel species in a new genus for which we propose the name Limisphaera ngatamarikiensis gen. nov., sp. nov. The type strain is NGM72.4(T) (?=?ICMP 20182(T)?=?DSM 27329(T)). PMID:25575826

  2. Thermoanaerobaculum aquaticum gen. nov., sp. nov., the first cultivated member of Acidobacteria subdivision 23, isolated from a hot spring.

    PubMed

    Losey, Nathaniel A; Stevenson, Bradley S; Busse, Hans-Jürgen; Sinninghe Damsté, Jaap S; Rijpstra, W Irene C; Rudd, Stephen; Lawson, Paul A

    2013-11-01

    A novel bacterium was isolated from a freshwater hot spring, the Hale House Spring, located at Hot Springs National Park, Hot Springs, AR, USA. Cells of strain MP-01(T) stained Gram-negative, were rod-shaped, non-motile, strictly anaerobic and chemo-organotrophic and did not form spores. Growth occurred at 50-65 °C, with an optimum at 60 °C, at pH 6.0-8.0, with an optimum at pH 6.5-7.0, and at NaCl concentrations up to 0.5?% (w/v), with optimum growth in the absence of NaCl. Strain MP-01(T) was capable of fermentative growth on pyruvate or proteinaceous substrates as well as reducing Fe(III) and Mn(IV). Major fatty acids were iso-C15?:?0, iso-C16?:?0, anteiso-C17?:?0 and iso-C17?:?0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and the major isoprenoid quinone was MK-10. In the polyamine pattern, sym-homospermidine was the predominant compound. The DNA G+C content was 62.7 mol%. Analysis of the 16S rRNA gene sequence of the isolate indicated that strain MP-01(T) represents the first reported cultivated member of subdivision 23 of the Acidobacteria. It is proposed that strain MP-01(T) represents a novel genus and species, for which the name Thermoanaerobaculum aquaticum gen. nov., sp. nov. is proposed. The type strain of Thermoanaerobaculum aquaticum is MP-01(T) (?=?DSM 24856(T)?=?JCM 18256(T)). PMID:23771620

  3. A new Late Cretaceous ginkgoalean reproductive structure Nehvizdyella gen. nov. from the Czech Republic and its whole-plant reconstruction.

    PubMed

    Kvacek, Jirí; Falcon-Lang, Howard J; Dasková, Jirina

    2005-12-01

    During the Mesozoic Era, gingkoaleans comprised a diverse and widespread group. Here we describe ginkgoalean fossils in their facies context from the Late Cretaceous (Cenomanian) Peruc-Korycany Formation of the Czech Republic and present a reconstruction of tree architecture and ecology. Newly described in this study is the ovuliferous reproductive structure, Nehvizdyella bipartita gen. et sp. nov. (Ginkgoales). This ovuliferous organ consists of a bifurcating axis, terminated by large cupule-like structures, probably homologous to the collar of the recent Ginkgo. Each cupule encloses an orthotropous ovule. In specimens with the early developmental stages preserved, the entire ovule and young seed, with the exception of the micropylar area, is embedded in the cupule. Mature seeds consist of sclerotesta and sarcotesta. Monosulcate pollen grains of Cycadopites-type are found adhering to the seeds. Although similar to Ginkgo in terms of its large size and reduced number of seeds, N. bipartita differs from the extant genus in having ovules completely enclosed in a cupule-like structure. The co-occurrence of N. bipartita with ginkgoalean leaves of Eretmophyllum obtusum (Velenovský) Kva?ek, J., ginkgoalean short shoots of Pecinovicladus kvacekii Falcon-Lang, and ginkgoalean trunk wood of Ginkgoxylon gruettii Pons and Vozenin-Serra in monodominant taphocoenoses at four geographically distant localities suggests that these remains all belong to one plant. This is supported by the close morphological and anatomical similarity between the different organs. Facies analysis of plant assemblages indicates that our Cretaceous tree occupied a water-stressed coastal salt marsh environment. It therefore represents the first unequivocal halophyte among the Ginkgoales. PMID:21646114

  4. Jatrophihabitans endophyticus gen. nov., sp. nov., an endophytic actinobacterium isolated from a surface-sterilized stem of Jatropha curcas L.

    PubMed

    Madhaiyan, Munusamy; Hu, Chuan Jiong; Kim, Soo-Jin; Weon, Hang-Yeon; Kwon, Soon-Wo; Ji, Lianghui

    2013-04-01

    A short rod-shaped Gram-stain-positive actinobacterium was isolated as an endophyte from the tissues of Jatropha curcas cv. KB27 and was investigated by means of a polyphasic taxonomic approach. An analysis of its 16S rRNA gene sequence indicated that strain S9-650(T) forms an individual line of descent and is related to certain members of the suborder Frankineae, order Actinomycetales (<95?% sequence similarity). Distance-matrix and neighbour-joining analyses set the branching point of the novel isolate between two clades, one being represented by members of the genera Frankia (family Frankiaceae) and Acidothermus (family Acidothermaceae) and the other by members of the genera Geodermatophilus, Blastococcus and Modestobacter (family Geodermatophilaceae). The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The acyl type was found to be N-glycolylated. The major menaquinone was MK-9(H4) and the fatty acid profile was characterized by the predominance of iso-C16?:?0, C18?:?1?9c, anteiso-C17?:?0 and C17?:?1?8c. The polar lipids comprised diphosphatidylglycerol, an unidentified glycolipid, phospholipids and aminolipids. The G+C content of the genomic DNA was 71.2 mol%. The distinct phylogenetic position and the phenotypic markers that clearly separate the novel organism from all other members of the suborder Frankineae indicate that strain S9-650(T) represents a novel species in a new genus, for which the name Jatrophihabitans endophyticus gen. nov., sp. nov. is proposed. The type strain of the type species is S9-650(T) (?=?DSM 45627(T)?=?KACC 16232(T)). PMID:22798659

  5. Exilispira thermophila gen. nov., sp. nov., an anaerobic, thermophilic spirochaete isolated from a deep-sea hydrothermal vent chimney.

    PubMed

    Imachi, Hiroyuki; Sakai, Sanae; Hirayama, Hisako; Nakagawa, Satoshi; Nunoura, Takuro; Takai, Ken; Horikoshi, Koki

    2008-10-01

    A novel thermophilic, anaerobic bacterium, strain RASEN(T), was isolated from a deep-sea hydrothermal vent chimney sample collected in the Iheya North field, Okinawa Trough, Japan, at a water depth of 982 m. The cells were motile, Gram-negative and helical with hooked ends, 0.23-0.28x15-27 microm in size with an approximate wavelength of 1.1-1.5 microm. Growth of the strain was observed at 37-60 degrees C (optimum 50 degrees C), in 2.5-3.5 % (w/v) NaCl (optimum 2.5-3 % NaCl) and at pH 6.0-7.5 (optimum pH 7.0). The strain grew on yeast extract only of the substrates examined in this study. The G+C content of the genomic DNA was 27.1 mol%. Major fatty acids for the strain were C(16 : 0), C(18 : 1)(Delta9) trans, C(18 : 0) and C(18 : 1)(Delta9) cis. Based on comparative 16S rRNA gene sequence analysis, strain RASEN(T) formed a deeply branching lineage within the phylum Spirochaetes and had only low levels of sequence similarity with other species of the phylum (range of similarity 72.1-80.6 %). Hence, we propose the name Exilispira thermophila gen. nov., sp. nov. The type strain of Exilispira thermophila is strain RASEN(T) (=JCM 14728(T) =NBRC 103205(T) =KCTC 5595(T)). PMID:18842837

  6. Methanolinea tarda gen. nov., sp. nov., a methane-producing archaeon isolated from a methanogenic digester sludge.

    PubMed

    Imachi, Hiroyuki; Sakai, Sanae; Sekiguchi, Yuji; Hanada, Satoshi; Kamagata, Yoichi; Ohashi, Akiyoshi; Harada, Hideki

    2008-01-01

    A novel methane-producing archaeon, strain NOBI-1(T) was isolated from an anaerobic, propionate-degradation enrichment culture, which was originally obtained from a mesophilic methanogenic sludge digesting municipal sewage sludge. Cells were non-motile, rod-shaped, 0.7-1.0 microm by 2.0 microm, and formed multicellular filaments longer than 8 microm. Growth was observed between 35 and 55 degrees C (optimum 50 degrees C) and pH 6.7 and 8.0 (optimum pH 7.0). The G+C content of the genomic DNA was 56.3 mol%. The strain utilized H(2) and formate for growth and methane production. Based on comparative sequence analyses of the 16S rRNA gene and mcrA gene (encoding the alpha subunit of methyl-coenzyme M reductase, a key enzyme in the methane-production pathway), strain NOBI-1(T) was affiliated with the order Methanomicrobiales, but it was significantly distant from any other known species within the order. The most closely related species based on 16S rRNA and mcrA gene sequence similarity were respectively 'Candidatus Methanoregula boonei' (93.7% 16S rRNA gene sequence similarity) and Methanocorpusculum parvum (74.2% deduced McrA amino acid sequence similarity to the type strain). These phenotypic and genetic properties justified the creation of a novel species of a new genus for the strain, for which we propose the name Methanolinea tarda gen. nov., sp. nov. The type strain of Methanolinea tarda is strain NOBI-1(T) (=DSM 16494(T) =JCM 12467(T) =NBRC 102358(T)). PMID:18175725

  7. Desulfitibacter alkalitolerans gen. nov., sp. nov., an anaerobic, alkalitolerant, sulfite-reducing bacterium isolated from a district heating plant.

    PubMed

    Nielsen, Marie Bank; Kjeldsen, Kasper Urup; Ingvorsen, Kjeld

    2006-12-01

    A novel alkalitolerant, anaerobic bacterium, designated strain sk.kt5(T), was isolated from a metal coupon retrieved from a corrosion-monitoring reactor of a Danish district heating plant (Skanderborg, Jutland). The cells of strain sk.kt5(T) were motile, rod-shaped (0.4-0.6 x 2.5-9.6 microm), stained Gram-positive and formed endospores. Strain sk.kt5(T) grew at pH 7.6-10.5 (with optimum growth at pH 8.0-9.5), at temperatures in the range 23-44 degrees C (with optimum growth at 35-37 degrees C), at NaCl concentrations in the range 0-5 % (w/v) (with optimum growth at 0-0.5 %) and required yeast extract for growth. Only a limited number of substrates were utilized as electron donors, including betaine, formate, lactate, methanol, choline and pyruvate. Elemental sulfur, sulfite, thiosulfate, nitrate and nitrite, but not sulfate or Fe(III) citrate, were used as electron acceptors. The G+C content of the DNA was 41.6 mol%. Phylogenetic analyses of the sequence data for the dsrAB genes [encoding the major subunits of dissimilatory (bi)sulfite reductase] and the 16S rRNA gene placed strain sk.kt5(T) within a novel lineage in the class Clostridia of the phylum Firmicutes. Taken together, the physiological and genotypic data suggest that strain sk.kt5(T) represents a novel species within a novel genus, for which the name Desulfitibacter alkalitolerans gen. nov., sp. nov. is proposed. The type strain of Desulfitibacter alkalitolerans is sk.kt5(T) (=JCM 12761(T)=DSM 16504(T)). PMID:17158984

  8. Calditerricola satsumensis gen. nov., sp. nov. and Calditerricola yamamurae sp. nov., extreme thermophiles isolated from a high-temperature compost.

    PubMed

    Moriya, Toshiyuki; Hikota, Tomohisa; Yumoto, Isao; Ito, Takashi; Terui, Yusuke; Yamagishi, Akihiko; Oshima, Tairo

    2011-03-01

    Two novel thermophilic micro-organisms, designated YMO81(T) and YMO722(T), were isolated from a high-temperature compost (internal temperature > 95 °C). The isolates were able to grow at 80 °C in a nutrient broth and in a synthetic medium. Cells were aerobic, Gram-negative rods (0.3 x 4.0 ?m). Spore formation was not observed. Strain YMO81(T) grew at 83 °C and pH 6.9-8.9 and grew optimally at 78 °C and pH 7.5 with 2 ?% NaCl. For growth in a synthetic minimal medium at 70 °C, the vitamins biotin, folic acid and thiamine and the amino acids glutamine and methionine were essential for growth of both strains; at 80 °C, strain YMO81(T) also required histidine, isoleucine, leucine, lysine, phenylalanine, serine, tryptophan and valine. Cellular fatty acids of the isolates comprised mainly iso-C??:? and anteiso-C??:?. The DNA G+C contents of strains YMO81(T) and YMO722(T) were 70 and 64 mol%, respectively. When the 16S rRNA gene sequences of the isolates were compared with those of other bacteria, highest similarity was observed with Planifilum yunnanense LA5(T) (90?% 16S rRNA gene sequence similarity). DNA-DNA relatedness between strain YMO722(T) and strain YMO81(T) was 55? %. N?-Aminopropylspermine was identified as a major polyamine, which suggested that the isolates were distinct from other related taxa. On the basis of phylogenetic, phenotypic and chemotaxonomic analyses, we propose a new genus, Calditerricola gen. nov., and two novel species, the type species Calditerricola satsumensis sp. nov., with type strain YMO81(T) (=ATCC BAA-1462(T) =JCM 14719(T) =DSM 45223(T)), and Calditerricola yamamurae sp. nov., with type strain YMO722(T) (=ATCC BAA-1461(T) =JCM 14720(T) =DSM 45224(T)). PMID:20400666

  9. Natribaculum breve gen. nov., sp. nov. and Natribaculum longum sp. nov., halophilic archaea isolated from saline soil.

    PubMed

    Liu, Qin; Ren, Min; Zhang, Li-Li

    2015-02-01

    Two halophilic archaeal strains, TRM20010(T) and TRM20345(T), were isolated from saline soil of the Lop Nur region in Xinjiang, north-west China. Cells from the two strains were pleomorphic rods, stained Gram-negative and produced red-pigmented colonies. Strains TRM20010(T) and TRM20345(T) were able to grow at 30-62 °C (optimum 37 °C), 0.9-5.1 M NaCl (optimum 2.6 and 3.4 M, respectively) and pH 6.0-10.0 (optimum pH 7.0-7.5) and neither strain required Mg(2+) for growth. The major polar lipids of the two strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), two glycolipids chromatographically identical to galactosyl mannosyl glucosyl diether (TGD-1) and disulfated mannosyl glucosyl diether (S2-DGD). Phylogenetic analysis based on 16S rRNA and rpoB' genes revealed that strains TRM20010(T) and TRM20345(T) clustered together and formed a distinct clade separated from the related genera Halovivax, Haloterrigena, Halostagnicola, Natronolimnobius and Natrinema. The DNA G+C contents of strains TRM20010(T) and TRM20345(T) were 63.9 and 63.8 mol%, respectively. The DNA-DNA hybridization value between strain TRM20010(T) and strain TRM20345(T) was 42.8 %. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strains TRM20010(T) and TRM20345(T) represent two novel species in a new genus within the family Halobacteriaceae, for which the names Natribaculum breve gen. nov., sp. nov. (type strain TRM20010(T)?= CCTCC AB2013112(T)?= NRRL B-59996(T)) and Natribaculum longum sp. nov. (type strain TRM20345(T)?= CCTCC AB2013113(T)?= NRRL B-59997(T)) are proposed. PMID:25406237

  10. Halomicroarcula pellucida gen. nov., sp. nov., a non-pigmented, transparent-colony-forming, halophilic archaeon isolated from solar salt.

    PubMed

    Echigo, Akinobu; Minegishi, Hiroaki; Shimane, Yasuhiro; Kamekura, Masahiro; Itoh, Takashi; Usami, Ron

    2013-10-01

    A novel halophilic strain, BNERC31(T), was isolated from solar salt, 'Sel marin de Guérande', imported from France. Colonies on agar medium containing soluble starch, sodium citrate, sodium glutamate and inorganic salts were non-pigmented and transparent, while cells obtained by centrifuging liquid cultures were red-pigmented. Cells of strain BNERC31(T) were non-motile, pleomorphic, stained Gram-negative and lysed in distilled water. Growth occurred with 20-30?% (w/v) NaCl (optimum, 25?%, w/v), with 0-500 mM MgCl2 (optimum, 10 mM), at pH 6.0-8.5 (optimum, pH 7.0) and at 25-55 °C (optimum, 40 °C). Growth was dependent on soluble starch, and inhibited completely by 0.5?% organic nutrients, such as Casamino acids or yeast extract. The DNA G+C content was 64.1 mol%. Strain BNERC31(T) possessed at least two heterogeneous 16S rRNA genes, and the sequence of the orthologous gene (preceded by the dihydroorotate oxidase gene, pyrD) showed the highest similarity (96.5?%) to that of Haloarcula marismortui JCM 8966(T). The RNA polymerase subunit B' gene sequence showed the highest similarity (91.7?%) to that of Haloarcula amylolytica JCM 13557(T). The polar lipids of strain BNERC31(T) were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, diglycosyl diether and sulfated diglycosyl diether, similar to those of species of the genus Halomicrobium. The phenotypic and phylogenetic characteristics showed that strain BNERC31(T) differed from species of the genera Haloarcula and Halomicrobium and indicated that it represents a novel species in a new genus, for which the name Halomicroarcula pellucida gen. nov., sp. nov. is proposed. The type strain of the type species is BNERC31(T) (?=?JCM 17820(T)?=?CECT 7537(T)). PMID:23563231

  11. Thermoterrabacterium ferrireducens gen. nov., sp. nov., a thermophilic anaerobic dissimilatory Fe(III)-reducing bacterium from a continental hot spring

    SciTech Connect

    Slobodkin, A.; Wiegel, J.; Reysenbach, A.L.

    1997-04-01

    A strain of a thermophilic, anaerobic, dissimilatory, Fe(III)-reducing bacterium, Thermoterrabacterium ferrireducens gen. nov., sp. nov. (type strain JW/AS-Y7{sup T}; DSM 11255), was isolated from hot springs in Yellowstone National Park and New Zealand. The gram-positive-staining cells occurred singly or in pairs as straight to slightly curved rods, 0.3 to 0.4 by 1.6 to 2.7 {mu}m, with rounded ends and exhibited a tumbling motility. Spores were not observed. The temperature range for growth was 50 to 74{degrees}C with an optimum at 65{degrees}C. The pH range for growth at 65{degrees}C was from 5.5 to 7.6, with an optimum at 6.0 to 6.2. The organism coupled the oxidation of glycerol to reduction of amorphous Fe(III) oxide or Fe(III) citrate as an electron acceptor. In the presence as well as in the absence of Fe(III) and in the presence of CO{sub 2}, glycerol was metabolized by incomplete oxidation to acetate as the only organic metabolic product; no H{sub 2} was produced during growth. The organism utilized glycerol, lactate, 1,2-propanediol, glycerate, pyruvate, glucose, fructose, mannose, and yeast extract as substrates. In the presence of Fe(III) the bacterium utilized molecular hydrogen. The organism reduced 9,10-anthraquinone-2,6-disulfonic acid, fumarate (to succinate), and thiosulfate (to elemental sulfur) but did not reduce MnO{sub 2}, nitrate, sulfate, sulfite, or elemental sulfur. The G+C content of the DNA was 41 mol% (as determined by high-performance liquid chromatography). The 16S ribosomal DNA sequence analysis placed the isolated strain as a member of a new genus within the gram-type positive Bacillus-Clostridium subphylum.

  12. Cellulosibacter alkalithermophilus gen. nov., sp. nov., an anaerobic alkalithermophilic, cellulolytic-xylanolytic bacterium isolated from soil of a coconut garden.

    PubMed

    Watthanalamloet, Amornrat; Tachaapaikoon, Chakrit; Lee, Yun Sik; Kosugi, Akihiko; Mori, Yutaka; Tanasupawat, Somboon; Kyu, Khin Lay; Ratanakhanokchai, Khanok

    2012-10-01

    An obligately anaerobic, cellulolytic-xylanolytic bacterium, designated strain A6(T), was isolated from soil of a coconut garden in the Bangkuntien district of Bangkok, Thailand. The strain was Gram-stain positive, catalase-negative, endospore-forming, motile and rod-shaped with a cell size of 0.2-0.3×2.0-3.0 µm. Optimal growth of strain A6(T) occurred at pH(55 °C) 9.5, 55 °C. Strain A6(T) fermented various carbohydrates, and the end products from the fermentation of cellobiose were acetate, ethanol, propionate and a small amount of butyrate. The major cellular fatty acids were iso-C(14:0) 3-OH, iso-C(15:0), iso-C(16:0) and C(16:0). The cell-wall peptidoglycan contained meso-diaminopimelic acid. No respiratory quinones were detected. The DNA G+C content was 30.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain represented a new phyletic sublineage within the family Clostridiaceae, with <93.0% 16S rRNA gene sequence similarity to recognized species of this family. On the basis of phenotypic, genotypic and physiological evidence, strain A6(T) represents a novel species of a new genus, for which the name Cellulosibacter alkalithermophilus gen. nov., sp. nov. is proposed. The type strain of the type species is A6(T) (?=?TISTR 1915(T)?=?KCTC 5874(T)). PMID:22140158

  13. Magnetospira thiophila gen. nov., sp. nov., a marine magnetotactic bacterium that represents a novel lineage within the Rhodospirillaceae (Alphaproteobacteria).

    PubMed

    Williams, Timothy J; Lefèvre, Christopher T; Zhao, Weidong; Beveridge, Terry J; Bazylinski, Dennis A

    2012-10-01

    A marine, magnetotactic bacterium, designated strain MMS-1(T), was isolated from mud and water from a salt marsh in Woods Hole, Massachusetts, USA, after enrichment in defined oxygen-concentration/redox-gradient medium. Strain MMS-1(T) is an obligate microaerophile capable of chemoorganoheterotrophic and chemolithoautotrophic growth. Optimal growth occurred at pH 7.0 and 24-26 °C. Chemolithoautotrophic growth occurred with thiosulfate as the electron donor and autotrophic carbon fixation was via the Calvin-Benson-Bassham cycle. The G+C content of the DNA of strain MMS-1(T) was 47.2 mol%. Cells were Gram-negative and morphologically variable, with shapes that ranged from that of a lima bean to fully helical. Cells were motile by means of a single flagellum at each end of the cell (amphitrichous). Regardless of whether grown in liquid or semi-solid cultures, strain MMS-1(T) displayed only polar magnetotaxis and possessed a single chain of magnetosomes containing elongated octahedral crystals of magnetite, positioned along the long axis of the cell. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MMS-1(T) belongs to the family Rhodospirillaceae within the Alphaproteobacteria, and is distantly related to species of the genus Magnetospirillum. Strain MMS-1(T) is therefore considered to represent a novel species of a new genus, for which the name Magnetospira thiophila gen. nov., sp. nov. is proposed. The type strain of Magnetospira thiophila is MMS-1(T) (?=?ATCC BAA-1438(T)?=?JCM 17960(T)). PMID:22140150

  14. Aestuariicella hydrocarbonica gen. nov., sp. nov., an aliphatic hydrocarbon-degrading bacterium isolated from a sea tidal flat.

    PubMed

    Lo, Naysim; Kim, Kyung Hyun; Baek, Kyunghwa; Jia, Baolei; Jeon, Che Ok

    2015-06-01

    A Gram-staining-negative, strictly aerobic bacterial strain, designated SM-6T, was isolated from a sea tidal flat of the Dangjin bay, South Korea. Strain SM-6T was able to degrade a broad range of aliphatic hydrocarbons. Cells were catalase- and oxidase-positive and non-motile rods. Growth of strain SM-6T was observed at 10-37 °C (optimum, 20-25 °C), at pH 5.5-9.0 (optimum, pH 6.5-7.5) and in the presence of 0-10 % (w/v) NaCl (optimum, 2-3 %). The only isoprenoid quinone detected was ubiquinone-8 (Q-8). C17:1?8c, C11:0 3-OH, summed feature 3 (comprising C16:1?7c and/or C16:1?6c), C9:0 3-OH and C10:0 3-OH were observed as the major cellular fatty acids and phosphatidylethanolamine, phosphatidylglycerol and four unidentified lipids were detected as polar lipids. The G+C content of the genomic DNA was 47.5 mol%. Strain SM-6T was most closely related to Pseudomaricurvus alkylphenolicus KU41GT (95.5 %), Maricurvus nonylphenolicus KU41ET (94.4 %) and Pseudoteredinibacter isoporae SW-11T (94.3 %), based on 16S rRNA gene sequences, and phylogenetic analyses showed that strain SM-6T formed a phyletic lineage distinct from the closely related genera. On the basis of phenotypic, chemotaxonomic and molecular features, strain SM-6T represents a novel genus and species of the order Alteromonadales in the class Gammaproteobacteria, for which name Aestuariicella hydrocarbonica gen. nov., sp. nov. is proposed. The type strain is SM-6T (?= KACC 18121T = JCM 30134T). PMID:25795067

  15. ‘Cand. Actinochlamydia clariae’ gen. nov., sp. nov., a Unique Intracellular Bacterium Causing Epitheliocystis in Catfish (Clarias gariepinus) in Uganda

    PubMed Central

    Steigen, Andreas; Nylund, Are; Karlsbakk, Egil; Akoll, Peter; Fiksdal, Ingrid U.; Nylund, Stian; Odong, Robinson; Plarre, Heidrun; Semyalo, Ronald; Skår, Cecilie; Watanabe, Kuninori

    2013-01-01

    Background and Objectives Epitheliocystis, caused by bacteria infecting gill epithelial cells in fish, is common among a large range of fish species in both fresh- and seawater. The aquaculture industry considers epitheliocystis an important problem. It affects the welfare of the fish and the resulting gill disease may lead to mortalities. In a culture facility in Kampala, Uganda, juveniles of the African sharptooth catfish (Clarias gariepinus) was observed swimming in the surface, sometimes belly up, showing signs of respiratory problems. Histological examination of gill tissues from this fish revealed large amounts of epitheliocysts, and also presence of a few Ichthyobodo sp. and Trichodina sp. Methods and Results Sequencing of the epitheliocystis bacterium 16S rRNA gene shows 86.3% similarity with Candidatus Piscichlamydia salmonis causing epitheliocystis in Atlantic salmon (Salmo salar). Transmission electron microscopy showed that the morphology of the developmental stages of the bacterium is similar to that of members of the family Chlamydiaceae. The similarity of the bacterium rRNA gene sequences compared with other chlamydia-like bacteria ranged between 80.5% and 86.3%. Inclusions containing this new bacterium have tubules/channels (termed actinae) that are radiating from the inclusion membrane and opening on the cell surface or in neighbouring cells. Conclusions Radiation of tubules/channels (actinae) from the inclusion membrane has never been described in any of the other members of Chlamydiales. It seems to be a completely new character and an apomorphy. We propose the name Candidatus Actinochlamydia clariae gen. nov., sp. nov. (Actinochlamydiaceae fam. nov., order Chlamydiales, phylum Chlamydiae) for this new agent causing epitheliocystis in African sharptooth catfish. PMID:23826156

  16. Oleiphilaceae fam. nov., to include Oleiphilus messinensis gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons.

    PubMed

    Golyshin, Peter N; Chernikova, Tatiana N; Abraham, Wolf-Rainer; Lünsdorf, Heinrich; Timmis, Kenneth N; Yakimov, Michail M

    2002-05-01

    A bacterial isolate, ME102T, was obtained from an n-hexadecane enrichment culture of seawater/sediment samples collected in the harbour of Messina (Italy). This gram-negative, aerobic, motile, rod-shaped bacterium used a narrow spectrum of organic compounds, including aliphatic hydrocarbons, alkanoates and alkanoles, as carbon and energy sources. None of the sugars, organic acids or amino acids tested was used. During cultivation on n-alkanes as the sole source of carbon and energy, the cells formed a biofilm on the surface of the alkane droplets. Large-scale (sometimes >50% of the cell mass) intracellular accumulation of alkanoates occurred in cells adsorbed on the alkane surface and under nitrogen-limiting conditions. 16S rRNA gene sequence analysis showed that this isolate represents a distinct lineage in the gamma-Proteobacteria and has about 91% sequence identity to members of Marinobacter and Alcanivorax, the closest genera. Four different types of polar lipid could be detected, phosphatidyl glycerol, phosphatidyl ethylamine, phosphatidyl dimethylethylamine and lipids belonging to an unknown type of phospholipid (m/z between 861 and 879). The principal fatty acids in the polar lipid fatty acid profile were 16:0 and 16:1. The putative gene encoding the key enzyme of alkane catabolism, alkane hydroxylase (AlkB), has been cloned. The protein sequence of the putative AlkB of the isolate ME102T was related to the AlkB of Pseudomonas oleovorans and Alcanivorax borkumensis, showing about 60% sequence identity. On the basis of physiological studies and taking into account the distant phylogenetic position of isolate ME102T relative to previously described organisms, a novel genus and species is proposed, Oleiphilus messinensis gen. nov., sp. nov., within a new family, Oleiphilaceae fam. nov. Strain ME102T (= DSM 13489T = LMG 20357T) is the type and only strain of O. messinensis. PMID:12054256

  17. Genomic and Physiological Characterization of the Verrucomicrobia Isolate Diplosphaera colitermitum gen. nov., sp. nov., Reveals Microaerophily and Nitrogen Fixation Genes

    PubMed Central

    Kim, Eunji; Breznak, John A.; Schmidt, Thomas M.; Rodrigues, Jorge L. M.

    2012-01-01

    Previously we reported the cultivation of novel verrucomicrobia, including strain TAV2 (93% 16S rRNA gene identity to its nearest cultivated representative, Opitutus terreae PB90-1) from the gut of the termite Reticulitermes flavipes. To gain better insight into the Verrucomicrobia as a whole and understand the role of verrucomicrobia within the termite gut ecosystem, we analyzed a draft genome and undertook a physiological characterization of TAV2. Strain TAV2 is an autochthonous member of the R. flavipes gut microbiota and groups phylogenetically among diverse Verrucomicrobia from R. flavipes and other termites that are represented by 16S rRNA gene sequences alone. TAV2 is a microaerophile, possessing a high-affinity cbb3-type terminal oxidase-encoding gene and exhibiting an optimum growth rate between 2 and 8% (vol/vol) oxygen. It has the genetic potential to degrade cellulose, an important function within termite guts, but its in vitro substrate utilization spectrum was limited to starch and a few mono- and disaccharides. Growth occurred on nitrogen-free medium, and genomic screening revealed genes for dinitrogenases, heretofore detected in only a few members of the Verrucomicrobia. This represents the first (i) characterization of a verrucomicrobial species from the termite gut, (ii) report of nif and anf genes in a nonacidophilic verrucomicrobial species, and (iii) description of a microaerophilic genotype and phenotype in this phylum of bacteria. The genetic and physiological distinctiveness of TAV2 supports its recognition as the type strain of a new genus and species, for which the name Diplosphaera colitermitum gen. nov., sp. nov., is proposed. PMID:22194293

  18. From Metagenomics to Pure Culture: Isolation and Characterization of the Moderately Halophilic Bacterium Spiribacter salinus gen. nov., sp. nov.

    PubMed Central

    León, María José; Fernández, Ana B.; Ghai, Rohit; Sánchez-Porro, Cristina; Rodriguez-Valera, Francisco

    2014-01-01

    Recent metagenomic studies on saltern ponds with intermediate salinities have determined that their microbial communities are dominated by both Euryarchaeota and halophilic bacteria, with a gammaproteobacterium closely related to the genera Alkalilimnicola and Arhodomonas being one of the most predominant microorganisms, making up to 15% of the total prokaryotic population. Here we used several strategies and culture media in order to isolate this organism in pure culture. We report the isolation and taxonomic characterization of this new, never before cultured microorganism, designated M19-40T, isolated from a saltern located in Isla Cristina, Spain, using a medium with a mixture of 15% salts, yeast extract, and pyruvic acid as the carbon source. Morphologically small curved cells (young cultures) with a tendency to form long spiral cells in older cultures were observed in pure cultures. The organism is a Gram-negative, nonmotile bacterium that is strictly aerobic, non-endospore forming, heterotrophic, and moderately halophilic, and it is able to grow at 10 to 25% (wt/vol) NaCl, with optimal growth occurring at 15% (wt/vol) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that strain M19-40T has a low similarity with other previously described bacteria and shows the closest phylogenetic similarity with species of the genera Alkalilimnicola (94.9 to 94.5%), Alkalispirillum (94.3%), and Arhodomonas (93.9%) within the family Ectothiorhodospiraceae. The phenotypic, genotypic, and chemotaxonomic features of this new bacterium showed that it constitutes a new genus and species, for which the name Spiribacter salinus gen. nov., sp. nov., is proposed, with strain M19-40T (= CECT 8282T = IBRC-M 10768T = LMG 27464T) being the type strain. PMID:24747894

  19. Olivibacter sitiensis gen. nov., sp. nov., isolated from alkaline olive-oil mill wastes in the region of Sitia, Crete.

    PubMed

    Ntougias, Spyridon; Fasseas, Constantinos; Zervakis, Georgios I

    2007-02-01

    A novel, Gram-negative, non-motile, non-sporulating, rod-shaped bacterium isolated from a viscous two-phase olive-oil mill waste ('alpeorujo') is described. The strain, designated AW-6T, is an obligate aerobe, forming irregular, pigmented creamy white colonies. The pH and temperature ranges for growth were pH 5-8 and 5-45 degrees C, with optimal pH and temperature for growth of pH 6-7 and 28-32 degrees C, respectively. Strain AW-6T was chemo-organotrophic and utilized mostly D+ -glucose, protocatechuate and D+ -xylose, followed by L-cysteine, D- -fructose, D+ -galactose, L-histidine, lactose, sorbitol and sucrose. Menaquinone-7 was detected in the respiratory chain of strain AW-6T. The major fatty acids of strain AW-6T were C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH, iso-C(15 : 0), iso-C(17 : 0) 3-OH and C(16 : 0). The closest phylogenetic relative of strain AW-6T was clone BIti35 (89.7 % 16S rRNA gene sequence similarity), while Sphingobacterium thalpophilum DSM 11723T was the closest recognized relative within the Sphingobacteriaceae (88.2 % similarity). Strain AW-6T showed a low level of DNA-DNA relatedness to S. thalpophilum DSM 11723T (33.8-37.0 %). The DNA G+C content of strain AW-6T was 45.6 mol%. Physiological and chemotaxonomic data further confirmed the distinctiveness of strain AW-6T from members of the genera Sphingobacterium and Pedobacter. Thus, strain AW-6T is considered to represent a novel species of a new genus within the family Sphingobacteriaceae, for which the name Olivibacter sitiensis gen. nov., sp. nov. is proposed. The type strain is AW-6T =DSM 17696T=CECT 7133T). PMID:17267986

  20. Leadbetterella byssophila gen. nov., sp. nov., isolated from cotton-waste composts for the cultivation of oyster mushroom.

    PubMed

    Weon, Hang-Yeon; Kim, Byung-Yong; Kwon, Soon-Wo; Park, In-Cheol; Cha, In-Bae; Tindall, Brian J; Stackebrandt, Erko; Trüper, Hans G; Go, Seung-Joo

    2005-11-01

    A bacterial strain, designated 4M15T, was isolated from cotton-waste composts used as mushroom cultivation in South Korea. Properties of this isolate were studied on the basis of physiological and biochemical characteristics, fatty acid profile, isoprenoid quinone, DNA G+C content and phylogenetic position based on 16S rRNA gene sequence analysis. The strain was found to form a distinct phylogenetic lineage related to the family 'Flexibacteraceae' within the phylum 'Bacteroidetes'. No recognized species showed >85 % 16S rRNA gene sequence similarity to strain 4M15T. The fatty acid profile of strain 4M15(T) included C(16 : 1)omega7c/iso-C(15 : 0) 2-OH (30.5 %), iso-C(15 : 0) (24.2 %), iso-C(15 : 0) 2-OH/C(16 : 1)omega7c (15.9), iso-C(17 : 0) 3-OH (10.5 %) and C(16 : 0) (5.6 %). The major isoprenoid quinone was menaquinone MK-7. The DNA G+C content was 33.0 mol%. Cells were Gram-negative, strictly aerobic, rod-shaped, non-motile, catalase-positive, oxidase-positive and flexirubin-positive. The strain hydrolysed aesculin, gelatin, starch and tyrosine. Several phenotypic tests could be used to differentiate strain 4M15T from other members of the family 'Flexibacteraceae'. On the basis of the data presented, strain 4M15T should be assigned to the phylum 'Bacteroidetes' as a novel genus and species, for which the name Leadbetterella byssophila gen. nov., sp. nov. is proposed. The type strain is 4M15T (=KACC 11308T=DSM 17132T). PMID:16280486

  1. Rasnitsynala sigambrorum gen. et sp. n., a small odonatopterid (“Eomeganisoptera”, “Erasipteridae”) from the early Late Carboniferous of Hagen-Vorhalle (Germany)

    PubMed Central

    Zessin, Wolfgang; Brauckmann, Carsten; Gröning, Elke

    2011-01-01

    Abstract Besides Erasipteroides valentini (Brauckmann in Brauckmann, Koch & Kemper, 1985), Zessinella siope Brauckmann, 1988, and Namurotypus sippeli Brauckmann & Zessin, 1989, Rasnitsynala sigambrorum gen. et sp. n. is the fourth species of the Odonatoptera from the early Late Carboniferous (Early Pennsylvanian: Namurian B, Marsdenian) deposits of the important Hagen-Vorhalle Konservat-Lagerstätte in Germany. With its wing-span of about 55 mm it is unusually small even for the “Eomeganisoptera”. Its venation resembles other small “Eomeganisoptera”, in particular Zessinella siope. This is why it is here assigned to the probably paraphyletic “Erasipteridae” Carpenter, 1939. PMID:22259266

  2. Hypsilara royi gen. n. and sp. n. (Coleoptera, Elmidae, Larainae) from Southern Venezuela, with a revised key to Larainae of the Western Hemisphere

    PubMed Central

    Maier, Crystal A.; Spangler, Paul J.

    2011-01-01

    Abstract Here we describe a new genus, for a new species of riffle beetle, Hypsilara royi gen. n. and sp. n., from the tepui Cerro de la Neblina in southern Venezuela. This new genus can be distinguished from all other laraine genera by its small size (ca. 4.5 mm) and the presence of a shallow, wide, V-shaped groove across the apical third of the pronotum. An updated key to the genera of Western Hemisphere Larainae is provided, along with information on habitat and collection methods for this taxon. PMID:21998500

  3. Non-contiguous finished genome sequence and description of Gorillibacterium massiliense gen. nov, sp. nov., a new member of the family Paenibacillaceae

    PubMed Central

    Keita, Mamadou Bhoye; Padhmanabhan, Roshan; Caputo, Aurélia; Robert, Catherine; Delaporte, Eric; Raoult, Didier; Fournier, Pierre-Edouard; Bittar, Fadi

    2014-01-01

    Strain G5T gen. nov., sp. nov. is the type strain of Gorillibacterium massiliense, a newly proposed genus within the family Paenibacillaceae. This strain, whose genome is described here, was isolated in France from a stool sample of a wild Gorilla gorilla subsp. gorilla from Cameroon. G. massiliense is a facultatively anaerobic, Gram negative rod. Here we describe the features of this bacterium, together with the complete genome sequence and annotation. The 5,546,433 bp long genome (1 chromosome but no plasmid) contains 5,145 protein-coding and 76 RNA genes, including 69 tRNA genes. PMID:25197465

  4. Effectiveness of a Cloning and Sequencing Exercise on Student Learning with Subsequent Publication in the National Center for Biotechnology Information GenBank

    PubMed Central

    Lau, Joann M.

    2009-01-01

    With rapid advances in biotechnology and molecular biology, instructors are challenged to not only provide undergraduate students with hands-on experiences in these disciplines but also to engage them in the “real-world” scientific process. Two common topics covered in biotechnology or molecular biology courses are gene-cloning and bioinformatics, but to provide students with a continuous laboratory-based research experience in these techniques is difficult. To meet these challenges, we have partnered with Bio-Rad Laboratories in the development of the “Cloning and Sequencing Explorer Series,” which combines wet-lab experiences (e.g., DNA extraction, polymerase chain reaction, ligation, transformation, and restriction digestion) with bioinformatics analysis (e.g., evaluation of DNA sequence quality, sequence editing, Basic Local Alignment Search Tool searches, contig construction, intron identification, and six-frame translation) to produce a sequence publishable in the National Center for Biotechnology Information GenBank. This 6- to 8-wk project-based exercise focuses on a pivotal gene of glycolysis (glyceraldehyde-3-phosphate dehydrogenase), in which students isolate, sequence, and characterize the gene from a plant species or cultivar not yet published in GenBank. Student achievement was evaluated using pre-, mid-, and final-test assessments, as well as with a survey to assess student perceptions. Student confidence with basic laboratory techniques and knowledge of bioinformatics tools were significantly increased upon completion of this hands-on exercise. PMID:19952101

  5. Zebragryllus Desutter-Grandcolas & Cadena-Casteñada, n.gen. a new Gryllinae genus from Eastern and Western Amazonia, South America (Orthoptera, Grylloidea, Gryllidae).

    PubMed

    Desutter-Grandcolas, Laure; Cadena-Castañeda, Oscar J; Jaiswara, Ranjana; Anso, Jeremy

    2014-01-01

    We describe a new genus of grylline cricket, Zebragryllus Desutter-Grandcolas & Cadena-Casteñada n. gen., from the Neotropical Region, using characters of morphology and male genitalia; genitalic characters clearly show that Zebragryllus n. gen. is closely related to Anurogryllus Saussure, 1878. Six species are described as new to science, originating from western (Peru, Colombia) and eastern (French Guiana) Amazonia: Zebragryllus fuscus Desutter-Grandcolas, n. sp., Z. guianensis Desutter-Grandcolas, n. sp., Z. intermedius Desutter-Grandcolas, n. sp., Zebragryllus nauta Desutter-Grandcolas, n. sp., Zebragryllus nouragui Desutter-Grandcolas, n. sp., and Zebragryllus wittoto Desutter-Grandcolas and Cadena-Casteñada, n. sp., type species of the genus. They are characterized by their size, coloration (shining black, most often with white patterns of coloration, hence the genus name), and male and female genitalia. The calling songs of Z. guianensis Desutter-Grandcolas, n. sp., Z. intermedius Desutter-Grandcolas, n. sp., Z. nouragui Desutter-Grandcolas, n. sp., and Z. wittoto Desutter-Grandcolas and Cadena-Casteñada, n. sp. are described. An identification key is proposed for both males and females. PMID:24871163

  6. The International Consortium on Lithium Genetics (ConLiGen): An Initiative by the NIMH and IGSLI to Study the Genetic Basis of Response to Lithium Treatment

    PubMed Central

    Schulze, Thomas G.; Alda, Martin; Adli, Mazda; Akula, Nirmala; Ardau, Raffaella; Bui, Elise T.; Chillotti, Caterina; Cichon, Sven; Czerski, Piotr; Del Zompo, Maria; Detera-Wadleigh, Sevilla D.; Grof, Paul; Gruber, Oliver; Hashimoto, Ryota; Hauser, Joanna; Hoban, Rebecca; Iwata, Nakao; Kassem, Layla; Kato, Tadafumi; Kittel-Schneider, Sarah; Kliwicki, Sebastian; Kelsoe, John R.; Kusumi, Ichiro; Laje, Gonzalo; Leckband, Susan G.; Manchia, Mirko; MacQueen, Glenda; Masui, Takuya; Ozaki, Norio; Perlis, Roy H.; Pfennig, Andrea; Piccardi, Paola; Richardson, Sara; Rouleau, Guy; Reif, Andreas; Rybakowski, Janusz K.; Sasse, Johanna; Schumacher, Johannes; Severino, Giovanni; Smoller, Jordan W.; Squassina, Alessio; Turecki, Gustavo; Young, L. Trevor; Yoshikawa, Takeo; Bauer, Michael; McMahon, Francis J.

    2010-01-01

    For more than half a decade, lithium has been successfully used to treat bipolar disorder. Worldwide, it is considered the first-line mood stabilizer. Apart from its proven antimanic and prophylactic effects, considerable evidence also suggests an antisuicidal effect in affective disorders. Lithium is also effectively used to augment antidepressant drugs in the treatment of refractory major depressive episodes and prevent relapses in recurrent unipolar depression. In contrast to many psychiatric drugs, lithium has outlasted various pharmacotherapeutic ‘fashions’, and remains an indispensable element in contemporary psychopharmacology. Nevertheless, data from pharmacogenetic studies of lithium are comparatively sparse, and these studies are generally characterized by small sample sizes and varying definitions of response. Here, we present an international effort to elucidate the genetic underpinnings of lithium response in bipolar disorder. Following an initiative by the International Group for the Study of Lithium-Treated Patients (www.IGSLI.org) and the Unit on the Genetic Basis of Mood and Anxiety Disorders at the National Institute of Mental Health, lithium researchers from around the world have formed the Consortium on Lithium Genetics (www.ConLiGen.org) to establish the largest sample to date for genome-wide studies of lithium response in bipolar disorder, currently comprising more than 1,200 patients characterized for response to lithium treatment. A stringent phenotype definition of response is one of the hallmarks of this collaboration. ConLiGen invites all lithium researchers to join its efforts. PMID:20453537

  7. Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France

    PubMed Central

    Sonet, Gontran; Jordaens, Kurt; Braet, Yves; Bourguignon, Luc; Dupont, Eréna; Backeljau, Thierry; De Meyer, Marc; Desmyter, Stijn

    2013-01-01

    Abstract Fly larvae living on dead corpses can be used to estimate post-mortem intervals. The identification of these flies is decisive in forensic casework and can be facilitated by using DNA barcodes provided that a representative and comprehensive reference library of DNA barcodes is available. We constructed a local (Belgium and France) reference library of 85 sequences of the COI DNA barcode fragment (mitochondrial cytochrome c oxidase subunit I gene), from 16 fly species of forensic interest (Calliphoridae, Muscidae, Fanniidae). This library was then used to evaluate the ability of two public libraries (GenBank and the Barcode of Life Data Systems – BOLD) to identify specimens from Belgian and French forensic cases. The public libraries indeed allow a correct identification of most specimens. Yet, some of the identifications remain ambiguous and some forensically important fly species are not, or insufficiently, represented in the reference libraries. Several search options offered by GenBank and BOLD can be used to further improve the identifications obtained from both libraries using DNA barcodes. PMID:24453564

  8. Anaerobium acetethylicum gen. nov., sp. nov., a strictly anaerobic, gluconate-fermenting bacterium isolated from a methanogenic bioreactor.

    PubMed

    Patil, Yogita; Junghare, Madan; Pester, Michael; Müller, Nicolai; Schink, Bernhard

    2015-10-01

    A novel strictly anaerobic, mesophilic bacterium was enriched and isolated with gluconate as sole substrate from a methanogenic sludge collected from a biogas reactor. Cells of strain GluBS11T stained Gram-positive and were non-motile, straight rods, measuring 3.0-4.5?×?0.8-1.2??m. The temperature range for growth was 15-37?°C, with optimal growth at 30?°C, the pH range was 6.5-8.5, with optimal growth at pH?7, and the generation time under optimal conditions was 60?min. API Rapid 32A reactions were positive for ?-galactosidase, ?-glucosidase and ?-glucosidase and negative for catalase and oxidase. A broad variety of substrates was utilized, including gluconate, glucose, fructose, maltose, sucrose, lactose, galactose, melezitose, melibiose, mannitol, erythritol, glycerol and aesculin. Products of gluconate fermentation were ethanol, acetate, formate, H2 and CO2. Neither sulfate nor nitrate served as an electron acceptor. Predominant cellular fatty acids (>10?%) were C14?:?0, C16?:?0, C16?:?1?7c/iso-C15?:?0 2-OH and C18?:?1?7c. The DNA G+C content of strain GluBS11T was 44.1?mol%. Phylogenetic analysis based on 16S rRNA gene sequence data revealed that strain GluBS11T is a member of subcluster XIVa within the order Clostridiales. The closest cultured relatives are Clostridium herbivorans (93.1?% similarity to the type strain), Clostridium populeti (93.3?%), Eubacterium uniforme (92.4?%) and Clostridium polysaccharolyticum (91.5?%). Based on this 16S rRNA gene sequence divergence (>6.5?%) as well as on chemotaxonomic and phenotypic differences from these taxa, strain GluBS11T is considered to represent a novel genus and species, for which the name Anaerobium acetethylicum gen. nov., sp. nov. is proposed. The type strain of Anaerobium acetethylicum is GluBS11T (?=?LMG 28619T?=?KCTC 15450T?=?DSM 29698T). PMID:26297346

  9. Anoxybacter fermentans gen. nov., sp. nov., a piezophilic, thermophilic, anaerobic, fermentative bacterium isolated from a deep-sea hydrothermal vent.

    PubMed

    Zeng, Xiang; Zhang, Zhao; Li, Xi; Zhang, Xiaobo; Cao, Junwei; Jebbar, Mohamed; Alain, Karine; Shao, Zongze

    2015-02-01

    A novel piezophilic, thermophilic, anaerobic, fermentative bacterial strain, designated strain DY22613(T), was isolated from a deep-sea hydrothermal sulfide deposit at the East Pacific Rise (GPS position: 102.6° W 3.1° S). Cells of strain DY22613(T) were long, motile rods (10 to 20 µm in length and 0.5 µm in width) with peritrichous flagella and were Gram-stain-negative. Growth was recorded at 44-72 °C (optimum 60-62 °C) and at hydrostatic pressures of 0.1-55 MPa (optimum 20 MPa). The pH range for growth was from pH 5.0 to 9.0 with an optimum at pH 7.0. Growth was observed in the presence of 1 to 8 % (w/v) sea salts and 0.65 to 5.2 % (w/v) NaCl, with optimum salt concentrations at 3.5 % for sea salts and at 2.3 % for NaCl. Under optimal growth conditions, the shortest generation time observed was 27 min (60 °C, 20 MPa). Strain DY22613(T) was heterotrophic, able to utilize complex organic compounds, amino acids, sugars and organic acids including peptone, tryptone, beef extract, yeast extract, alanine, glutamine, methionine, phenylalanine, serine, threonine, fructose, fucose, galactose, gentiobiose, glucose, mannose, melibiose, palatinose, rhamnose, turanose, pyruvate, lactic acid, methyl ester, erythritol, galacturonic acid and glucosaminic acid. Strain DY22613(T) was able to reduce Fe(III) compounds, including Fe(III) oxyhydroxide (pH 7.0), amorphous iron(III) oxide (pH 9.0), goethite (?-FeOOH, pH 12.0), Fe(III) citrate and elementary sulfur. Products of fermentation were butyrate, acetate and hydrogen. Main cellular fatty acids were iso-C15 : 0, iso-C14 : 0 3-OH and C14 : 0. The genomic DNA G+C content of strain DY22613(T) was 36.7 mol%. Based on 16S rRNA gene sequence analysis, the strain forms a novel lineage within the class Clostridia and clusters with the order Haloanaerobiales (86.92 % 16S rRNA gene sequence similarity). The phylogenetic data suggest that the lineage represents at least a novel genus and species, for which the name Anoxybacter fermentans gen. nov., sp. nov. is proposed. The type strain is DY22613(T) (?= JCM 19466(T)?= DSM 28033(T)?= MCCC 1A06456(T)). PMID:25505345

  10. Planctomicrobium piriforme gen. nov., sp. nov., a stalked planctomycete from a littoral wetland of a boreal lake.

    PubMed

    Kulichevskaya, Irina S; Ivanova, Anastasia A; Detkova, Ekaterina N; Rijpstra, W Irene C; Sinninghe Damsté, Jaap S; Dedysh, Svetlana N

    2015-05-01

    An aerobic, budding, non-pigmented and rosette-forming bacterium was isolated from a littoral wetland of a boreal lake located in Valaam Island, northern Russia, and designated strain P3(T). Ellipsoidal to pear-shaped cells of this bacterium were covered with crateriform pits and possessed stalks suggesting a planctomycete morphotype. 16S rRNA gene sequence analysis confirmed that strain P3(T) was a member of the order Planctomycetales and belonged to a phylogenetic lineage defined by the genus Planctomyces , with 89 and 86% sequence similarity to Planctomyces brasiliensis and Planctomyces maris , respectively. Strain P3(T) was a mildly acidophilic, mesophilic organism capable of growth at pH values between pH 4.2 and 7.1 (with an optimum at pH 6.0-6.5) and at temperatures between 10 and 30 °C (optimum at 20-28 °C). Most sugars, a number of polysaccharides and several organic acids were the preferred growth substrates. Compared with Planctomyces brasiliensis and Planctomyces maris , which require NaCl for growth, strain P3(T) was salt-sensitive and did not develop at NaCl concentrations above 0.5% (w/v). The major fatty acids were C16 : 0 and C16 : 1?7c; the cells also contained significant amounts of C18 : 1?7c and C18 : 0. The major intact polar lipids were diacylglycerol-O-(N,N,N-trimethyl)homoserine (DGTS) lipids; the major neutral lipids were long-chain 1,(?-1)-diols and C31 : 9 hydrocarbon. The quinone was MK-6, and the G+C content of the DNA was 59.0 mol%. Strain P3(T) differed from Planctomyces brasiliensis and Planctomyces maris by cell morphology, substrate utilization pattern and a number of physiological characteristics. Based on these data, the novel isolate should be considered as representing a novel genus and species of planctomycetes, for which the name Planctomicrobium piriforme gen. nov., sp. nov., is proposed. The type strain is P3(T) (?=DSM 26348(T)?=VKM B-2887(T)). PMID:25724745

  11. Otariodibacter oris gen. nov., sp. nov., a member of the family Pasteurellaceae isolated from the oral cavity of pinnipeds.

    PubMed

    Hansen, Mie Johanne; Bertelsen, Mads Frost; Christensen, Henrik; Bojesen, Anders Miki; Bisgaard, Magne

    2012-11-01

    A total of 27 bacterial isolates from California sea lions and a walrus tentatively classified within the family Pasteurellaceae was further characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the isolates investigated formed a monophyletic group, tentatively designated Bisgaard taxon 57. According to 16S rRNA gene sequences, the most closely related species with a validly published name was Bisgaardia hudsonensis and the most closely related species based on rpoB sequence comparison was Pasteurella multocida subsp. multocida; highest similarities between the isolates and the type strains of B. hudsonensis and P. multocida subsp. multocida were 95.0 and 88.2%. respectively. All isolates of Bisgaard taxon 57 exhibit the phenotypic characters of the family Pasteurellaceae. Members of Bisgaard taxon 57 can be separated from existing genera of the Pasteurellaceae by the following tests: positive reactions for catalase, oxidase, Voges-Proskauer and indole; no X- or V-factor dependency; and acid production from L-arabinose (slow), L-fucose, maltose and trehalose, but not from dulcitol, D-mannitol, D-mannose or sucrose. The main fatty acids of Bisgaard taxon 57 (CCUG 59994(T)) are C(14:0), C(16:0), C(16:1)?7c and the summed feature C(14:0) 3-OH/iso-C(16:1) I. This fatty acid profile is characteristic of members of the Pasteurellaceae. The quinone profile of Bisgaard taxon 57 (DSM 23800(T)) was similar to that of other genera in the Pasteurellaceae. The DNA G+C content of strain Baika1(T) is 36.2 mol%, which is at the lower end of the range for members of the family Pasteurellaceae. On the basis of both phylogenetic and phenotypic evidence, it is proposed that members of Bisgaard taxon 57 should be classified as representatives of a novel species in a new genus, Otariodibacter oris gen. nov., sp. nov. The type strain of Otariodibacter oris is Baika1(T) (=CCUG 59994(T)=DSM 23800(T)), which was isolated from the oral cavity of a healthy California sea lion in Copenhagen Zoo, Denmark, in 2007. PMID:22199211

  12. Arachidicoccus rhizosphaerae gen. nov., sp. nov., a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil.

    PubMed

    Madhaiyan, Munusamy; Poonguzhali, Selvaraj; Senthilkumar, Murugaiyan; Pragatheswari, Dhandapani; Lee, Jung-Sook; Lee, Keun-Chul

    2015-02-01

    Three novel bacterial strains, designated Vu-144(T), Vu-7 and Vu-35, were isolated on minimal medium from rhizosphere soil of field-grown cowpea and subjected to a taxonomic study using a polyphasic approach. Cells of the strains were Gram-stain-negative, non-motile, non-spore-forming, coccoid rods, and formed non-pigmented colonies. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Vu-144(T) was affiliated with an uncultivated lineage of the phylum Bacteroidetes. Its closest phylogenetic neighbour was the recently described species Niastella populi, a member of the family Chitinophagaceae, with just 90.7 % sequence similarity to the type strain. The only isoprenoid quinone detected was menaquinone 7 (MK-7). The fatty acid profiles showed large amounts of iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G and minor amounts of summed feature 3 (C16 : 1?7c and/or iso-C15 : 0 2-OH), C16 : 0 and other fatty acids, allowing the differentiation of the strains from other genera. The G+C content of the genomic DNA of the three strains ranged from 43.1 to 44.3 mol%. In addition to phosphatidylethanolamine, the major polar lipids were three unidentified aminophospholipids (APL1-APL3), two unidentified phospholipids (PL1, PL2) and three unidentified lipids (UL1-UL3). Biochemical test patterns also differed from those of Niastella populi and members of other genera. All three isolates showed plant-growth-promoting properties, e.g. the ability to produce indole-3-acetic acid and NH3 and to solubilize phosphate, utilized 1-aminocyclopropane 1-carboxylate (ACC) as a sole source of nitrogen and possessed the ACC deaminase enzyme. The novel isolates readily colonized roots and stimulated growth of tomato and cowpea under glasshouse conditions. Inoculated plants showed a 45-60 % increase in dry matter weight with respect to uninoculated controls. On the basis of the evidence from our polyphasic study, isolate Vu-144(T) represents a novel genus and species in the family Chitinophagaceae, for which the name Arachidicoccus rhizosphaerae gen. nov., sp. nov. is proposed. The type strain of Arachidicoccus rhizosphaerae is Vu-144(T) (?= KCTC 22378(T)?= NCIMB 14473(T)). PMID:25404481

  13. Murimonas intestini gen. nov., sp. nov., an acetate-producing bacterium of the family Lachnospiraceae isolated from the mouse gut.

    PubMed

    Kläring, Karoline; Just, Sarah; Lagkouvardos, Ilias; Hanske, Laura; Haller, Dirk; Blaut, Michael; Wenning, Mareike; Clavel, Thomas

    2015-03-01

    Three strains of an anaerobic, Gram-stain-positive coccobacillus were isolated from the intestines of mice. These strains shared 100?% similarity in their 16S rRNA gene sequences, but were distantly related to any described members of the family Lachnospiraceae (<94?%). The most closely related species with names that have standing in nomenclature were Robinsoniella peoriensis, Ruminococcus gnavus, Blautia producta and Clostridium xylanolyticum. Phylogenetic relationships based on 16S rRNA gene sequence analysis were confirmed by partial sequencing of hsp60 genes. The use of an in-house database search pipeline revealed that the new isolates are most prevalent in bovine gut samples when compared with human and mouse samples for Ruminococcus gnavus and B. producta. All three isolated strains shared similar cellular fatty acid patterns dominated by C16?:?0 methyl ester. Differences in the proportions of C12?:?0 methyl ester, C14?:?0 methyl ester and C18?:?1 cis-11 dimethyl acetal were observed when compared with phylogenetically neighbouring species. The major short-chain fatty acid produced by strain SRB-530-5-H(T) was acetic acid. This strain tested positive for utilization of d-fructose, d-galacturonic acid, d-malic acid, l-alanyl l-threonine and l-glutamic acid but was negative for utilization of amygdalin, arbutin, ?-d-glucose, 3-methyl d-glucose and salicin, in contrast to the type strain of the closest related species Robinsoniella peoriensis. The isolates were not able to use mannitol for growth. Based on genotypic, phenotypic and chemotaxonomic characteristics, we propose to create the new genus and species Murimonas intestini gen. nov., sp. nov. to accommodate the three strains SRB-530-5-H(T) (?=?DSM 26524(T)?=?CCUG 63391(T)) (the type strain of Murimonas intestini), SRB-509-4-S-H (?=?DSM 27577?=?CCUG 64595) and SRB-524-4-S-H (?=?DSM 27578?=?CCUG 64594). PMID:25519299

  14. Anaerovirgula multivorans gen. nov., sp. nov., a Novel Spore-Forming, Alkaliphilic Anaerobe Isolated from Owens Lake, California, USA

    NASA Technical Reports Server (NTRS)

    Pikuta, Elena V.; Itoh, Takashi; Krader, Paul; Whitman, William B.; Hoover, Richard B.

    2006-01-01

    A novel, alkaliphilic, obligately anaerobic bacterium, strain SCAT, was isolated from mud sediments of a soda lake in California, USA. The rod-shaped cells were motile, Gram-positive, formed spores and were 0.4-0.5x2.5-5.0 micrometers in size. Growth occurred within the pH range 6.7-10.0 and was optimal at pH 8.5. The temperature range for growth was 10-45 degrees C, with optimal growth at 35 degrees C. NaCl was required for growth. Growth occurred at 0.5-9.0% (w/v) NaCl and was optimal at 1-2% (w/v). The novel isolate was a catalase-negative chemo-organoheterotroph that fermented sugars, proteolysis products, some organic and amino acids, glycerol, d-cellobiose and cellulose. It was also capable of growth by the Stickland reaction. Strain SCAT was sensitive to tetracycline, chloramphenicol, rifampicin and gentamicin, but it was resistant to ampicillin and kanamycin. The G+C content of the genomic DNA was 34.2 mol%. Major fatty acid components were C14:0, iso-C15:0, C16:1omega9c and C16:0. 16S rRNA gene sequence analysis of strain SCAT showed a similarity of approximately 97% with the type strains of Clostridium formicaceticum and Clostridium aceticum in clostridial cluster XI and a similarity of less than 94.2% to any other recognized Clostridium species and those of related genera in this cluster. Strain SCAT was clearly differentiated from C. formicaceticum and C. aceticum based on comparison of their phenotypic properties and fatty acid profiles, as well as low levels of DNA-DNA relatedness between strain SCAT and the type strains of these two species. Therefore, strain SCAT is considered to represent a novel species of a new genus, Anaerovirgula multivorans gen. nov., sp. nov., in clostridial cluster XI. The type strain is SCAT (=ATCC BAA-1084T=JCM 12857T=DSM 17722T=CIP 107910T).

  15. Anaerosolibacter carboniphilus gen. nov., sp. nov., a strictly anaerobic iron-reducing bacterium isolated from coal-contaminated soil.

    PubMed

    Hong, Heeji; Kim, So-Jeong; Min, Ui-Gi; Lee, Yong-Jae; Kim, Song-Gun; Roh, Seong Woon; Kim, Jong-Geol; Na, Jeong-Geol; Rhee, Sung-Keun

    2015-05-01

    A strictly anaerobic, mesophilic, iron-reducing bacterial strain, IRF19(T), was isolated from coal-contaminated soil in the Republic of Korea. IRF19(T) cells were straight, rod-shaped, Gram-staining-negative and motile by means of flagella. The optimum pH and temperature for their growth were determined to be pH 7.5-8.0 and 40 °C, while the optimum range was pH 6.5-10.0 and 20-45 °C, respectively. Strain IRF19(T) did not require NaCl for growth but it tolerated up to 2% (w/v). Growth was observed with yeast extract, D-glucose, D-fructose, D-ribose, D-mannitol, D-mannose, L-serine, L-alanine and L-isoleucine. Fe(III), elemental sulfur, thiosulfate and sulfate were used as electron acceptors. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain IRF19(T) is affiliated to the family Clostridiaceae and is most closely related to Salimesophilobacter vulgaris Zn2(T) (93.5% similarity), Geosporobacter subterraneus VNs68(T) (93.2%) and Thermotalea metallivorans B2-1(T) (92.3%). The major cellular fatty acids of strain IRF19(T) were C14 : 0, iso-C15 : 0 and C16?:?0, and the profile was distinct from those of the closely related species. The major respiratory quinone of strain IRF19(T) was menaquinone MK-5 (V-H2). The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid and two unknown polar lipids. The G+C content of the genomic DNA of strain IRF19(T) was determined to be 37.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic results, strain IRF19(T) is considered to represent a novel species of a novel genus of the family Clostridiaceae , for which we propose the name Anaerosolibacter carboniphilus gen. nov., sp. nov., with the type strain IRF19(T) (?=KCTC 15396(T)?=JCM 19988(T)). PMID:25701849

  16. Left ventricular systolic dysfunction in a biracial sample of hypertensive adults: The Hypertension Genetic Epidemiology Network (HyperGEN) Study.

    PubMed

    Devereux, R B; Bella, J N; Palmieri, V; Oberman, A; Kitzman, D W; Hopkins, P N; Rao, D C; Morgan, D; Paranicas, M; Fishman, D; Arnett, D K

    2001-09-01

    To determine the prevalence and correlates of left ventricular systolic dysfunction in hypertensive patients in a biracial population-based sample, clinical evaluation and echocardiography were performed in 2086 participants in the Hypertension Genetic Epidemiology Network (HyperGEN) examination; 86% had normal ejection fraction (>54%), 10% had mild ventricular dysfunction (ejection fraction 41% to 54%), and 4% had severe ventricular dysfunction (ejection fraction

  17. 267USDA Forest Service Gen.Tech.Rep. PSW-GTR-166. 1998. About 886.5 Mha in Russia is occupied by forests, including 763.5 Mha of tree stands and 123 Mha of non-

    E-print Network

    267USDA Forest Service Gen.Tech.Rep. PSW-GTR-166. 1998. Abstract About 886.5 Mha in Russia is occupied by forests, including 763.5 Mha of tree stands and 123 Mha of non- stocked lands. The Russian forests comprise about 22 percent of the earth's forest area or 43 percent of the earth's temperate

  18. 293USDA Forest Service Gen.Tech.Rep. PSW-GTR-166. 1998. Slovakia is a mountainous and forested country (40.6 percent forest cover) in central Europe and has a large

    E-print Network

    293USDA Forest Service Gen.Tech.Rep. PSW-GTR-166. 1998. Abstract Slovakia is a mountainous and forested country (40.6 percent forest cover) in central Europe and has a large variety of vegetation zones, forest types, and a rich diversity of forest tree species. The most important tree species are beech

  19. 65USDAForestServiceGen.Tech.Rep.PSW-GTR-166.1998. Ozone measurements are presented from the Bulgarian Govedartsi ecosystem study site, Ovnarsko No. 3. The site is

    E-print Network

    65USDAForestServiceGen.Tech.Rep.PSW-GTR-166.1998. Abstract Ozone measurements are presented from. There are no anthropogenic sources for ozone precursors for at least 30 km in all directions. Ozone concentrations within that occur during high pressure synoptic weather conditions. In these cases a thin stable cold layer

  20. The yeast genus Tortispora gen. nov., description of Tortispora ganteri sp. nov., Tortispora mauiana f.a., sp. nov., Tortispora agaves f.a., sp. nov., Tortispora sangerardii f.a., sp. nov.,...

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We describe the yeast genus Tortispora gen. nov., an early diverging lineage in the Saccharomycetales that features the formation of helical ascospores. The genus is based on 16 strains resembling Candida caseinolytica that were isolated from necrotic plant tissue in warm regions of the New World. B...